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From: "Leo W. Little" <>
Subject: Little SNP aka Null at DYS439
Date: Wed, 16 Nov 2005 07:23:08 -0800 (PST)


Dear List,

For those of you who are members of the ISOGG yahoo group, there was a thread on the "Little SNP aka Null at DYS439" starting on Monday. To summarize:

At the FTDNA conference, Taylor Edwards of the University of Arizona briefly mentioned the so-called "Little SNP" which lies in the flanking region of DYS439.

The SNP is so-named because it first appeared in the Little DNA project.

The "Little SNP" inhibits the FTDNA primers from initiating PCR of genetic material at DYS439, so folks with the SNP appear to have a null allele for that marker.

It appears the "Little SNP" is downstream of M269, so males who are found to have a "null439" are most likely members of a small subclade of R1b1c. So far, it appears the "null439" only occurs in about one out of a thousand males.

Null439s are now indicated directly in Family Tree DNA databases as follows:

For personal results, go to www.familytreedna.com and enter your Kit Number and Password under "MY FTDNA" on the right side of the page.

Click on the "Y-DNA DYS Values" tab and scroll down to DYS# 439. A null will be indicated by a blue asterisk with the following linked note at the bottom of the page:

*System assigned value. Your DNA sample produced no result for DYS 439.

The link takes you to http://www.familytreedna.com/DYS439Explanation.html which has the following text from Family Tree DNA:

> What does the blue * mean on my DYS values page?

> The lab has run your sample at least 2, and possible up to 4 times for DYS 439 and it has failed to run, so they have called it a NULL value.

> Because our matching system will not work with a Null value we have calculated the presumed value of your DYS 439 based upon how closely you match with others in our database that you share an identical profile with…who otherwise have a value at DYS 439.

> The lab is looking at this interesting situation and will have some news on this in 2006. When we have an update for you on this we’ll place it on this page linked form your results page at the web site.

> Mr. Leo Little has been looking at people who have this null reported value and can be contacted at

FTDNA project administrators can go to their respective Group Administrator Pages and select the "Generate Y-DNA Results for Copy & Paste" option. Null439 results will then be indicated by a "blue 12" in the DYS439 column.

http://www.geocities.com/null439/ has a description of the null439 phenomenon with links to results and phylograms. TMRCA for the group as a whole is about 2000 years (possible clusters have more recent TMRCA).

All of the surnames (except Abeyta) discovered to date appear to have British origins. An analysis of the surnames suggests a weak link to SW England, though given the subclade is likely 2000+ in age, more recent orgins could be anywhere.

"Abeyta" is of Basque/Spanish origin and the "null Abeyta" listings appear in the Santa Fe DNA project at http://www.familytreedna.com/public/NuevoMexico/ . I'm waiting to hear from the project administrator for more on the family ancestry.

If the "null Abeytas" can definitively be traced back to Iberia, then the origin of the null439s may be considerably older than just 2000 years.

The phylograms on http://www.geocities.com/null439/Phylogram.htm show possible connections between null439s participants, but are very sensitive to how the data is organized. Markers such as DYS464 and differences in marker mutation rates bring in question the accuracy of these diagrams, but they suggest a loose structure, and a relatively early origins of the sub-clade.

My thanks to Bennett at Family Tree DNA who has been extremely helpful in the understanding of the null439 phenomenon. Joe and Neal Fox have also been tireless in the search and analysis of null439 results.

Please post to the list or contact me directly if you have nulls at DYS439 in your respective projects. Two new null439s have come to light based on the posting in the ISOGG group (and thanks to Katherine Borges for her support on the null439 issue).

The null439 phenomenon is of specific interest to a few of us, but should be of general interest to anyone doing research on genetic diversity within subclades. It also shows the power of a combination STR-SNP approach to DNA testing.

Best Regards, Leo

Leo W. Little
Administrator,
Little DNA project, et al










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