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SNP Analysis


Because Single Nucleotide Polymorphisms ("SNPs") mutate less often and more predictably than Standard Tandem Repeats ("STRs"), SNPs will ultimately be more reliable than STRs in identifying the genealogical relationships among individual R1a1a Ashkenazi Levites (assuming that a sufficient sample of R1a1a Ashkenazi Levites do full Y-DNA sequencing) and should provide additional insight into the relationship of R1a1a Ashkenazi Levites to their closest matches who are not R1a1a Ashkenazi Levites. (Click here for Anatole Klyosov's criticism of and analysis concerning statements made on this page of the website.)

As discussed below, the handful of results of full Y-DNA sequencing that have been received to date (from private testing and tests performed for scientific study) have allowed the identification of SNPs that appear to define (1) R1a1a Ashkenazi Levites as a whole, (2) men who are close to the R1a1a Ashkenazi Levite mode, and (3) men who are known or likely descendants of the Horowitz rabbinical family. 

Those results have allowed the preliminary calculation of the age of clusters of R1a1a Ashkenazi Levites, based upon the SNPs shared by each cluster. Click here for preliminary calculations of the age of these clusters.

As each additional R1a1a Ashkenazi Levite receives full Y-DNA sequencing results, we will be able to define SNP-based branches with greater specificity and to calculate with greater certainty the time to the MRCA shared by each tested branch with each other tested branch. 

Click here for a schematic tree showing the SNP test results received to date for R1a1a Ashkenazi Levites. The tree identifies SNPs at or below the level of Z2469/CTS6+, the level of SNPs now believed to identify R1a1a Ashkenazi Levites and their closest match. 

Click here for a list of men who have received SNP results for R1a1a Ashkenazi Levite-specific SNPs offered for a la carte testing by FTDNA.

SNPs that Distinguish R1a1a Ashkenazi Levites

Currently, R1a1a Ashkenazi Levites are characterized by the SNPs Z93+ Z94+ Z2124+ Z2122+ F1345+ Z2469/CTS6+ (and probably Y2619+), going from upstream to downstream. These SNPs are characteristic of all R1a1a Ashkenazi Levites who have tested such SNPs. (Click here for a discussion of FTDNA's varying Y-DNA haplogroup designations for R1a1a Ashkenazi Levites.)

As of July 2014, following the receipt of the initial full Y-DNA test results from Full Genomes Corp. and FTDNA's Big Y test, Y-DNA results from Scotland's DNA, and scientific studies (Rootsi & Behar's 2013 paper and the Personal Genomes Project), and analysis by Full Genomes Corp. (in particular, Leon Kull), Vladimir Tagankin of YFull, and Michał Milewski and Mariusz Wilkoszewski of the FTDNA R1a1a and Subclades Y-DNA Project, we now know the following information concerning R1a1a Ashkenazi Levite SNPs. (For historical information relating to the identification of SNPs that are found in R1a1a Ashkenazi Levites and their closest matches or in R1a1a Ashkenazi Levites alone, click here.)

SNPs Shared by R1a1a Ashkenazi Levites and Their Iberian Match (CTS6 Level)

We have now identified 11 SNPs that are shared by R1a1a Ashkenazi Levites and their Iberian match that are located downstream from Z2472/F1345/FGC99 and F2997 (SNPs shared by R1a1a Ashkenazi Levites and their Iberian match with their next closest match, Kussad (116213), who is F1345+ Z2469/CTS6-). This website posts a tree and a table showing the SNPs that are currently grouped at the CTS6 level.

SNPs Shared by R1a1a Ashkenazi Levites but Not Their Iberian Match (Y2619 Level)

We have now identified 22 SNPs that are shared by all R1a1a Ashkenazi Levites who have done full Y-DNA testing but not by their Iberian match, i.e., they are at the Y2619 level. Further Y-DNA testing is likely to identify some R1a1a Ashkenazi Levites who do not share some of these SNPs; however, based upon a la carte testing of R1a1a Ashkenazi Levites with broadly varying patterns of STR marker values, it appears that Y2619 is characteristic of all R1a1a Ashkenazi Levites. This website posts a tree and a table showing the SNPs that are currently grouped at the CTS6 level.
                                                               
SNPs that Define Branches of the R1a1a Ashkenazi Levite Tree

As of July 31, 2014, we have seven sets of full Y-DNA test results for R1a1a Ashkenazi Levites. Click here for further information concerning the tested men.

SNPs Shared by R1a1a Ashkenazi Levites Who are Close to the Mode (Y2630 Level, YP467 Level, and YP264/YP265 Level)

There are three SNPs - currently designated as being at the Y2630 level - that are shared by a cluster of men whose STR test results are close to the R1a1a Ashkenazi Levite mode. 

Downstream from the Y2630 level is a Double Nucleotide Polymorphism ("DNP") that consists of two mutated alleles that are directly adjacent to each other. The DNP previously was given two SNP designations, YP467 and YP468; they now share a single DNP designation, YP467, that defines a new level between the Y2630 level and the YP264/YP265 level. 

There are five SNPs - currently designated as being at the YP264/YP265 level - that appear to be shared by R1a1a Ashkenazi Levites with the characteristic Horowitz STR marker value DYS495=16. (At least one of those five SNPs - YP264 - has also been found in some R1a1a Ashkenazi Levites who have DYS495=17 yet are YP264+, indicating that the mutation YP264+ pre-dated the mutation from DYS495=16 to DYS495=17 on the main Horowitz line.)

This website posts a tree and a table showing the SNPs that are currently grouped at the Y2630, YP467, and YP264/YP265 levels.

Currently Private SNPs

The men who have done full Y-DNA testing also have a varying number of private SNPs - SNPs that are not currently shared with any other man. If another R1a1a Ashkenazi Levite is tested and is found to share an SNP that is currently private, those SNPs will be known to define a branch of the R1a1a Ashkenazi Levite family tree and, as a result, will no longer be deemed private.

This website posts a tree and a table showing the SNPs that are currently private.

The Path Forward

As additional R1a1a Ashkenazi Levites are tested and receive test results, we should be able to identify SNPs that are characteristic of smaller branches of R1a1a Ashkenazi Levites. For example, as we receive test results from at least two men who are farther from the mode but are relatively close to each other, we should be able to identify SNPs that are characteristic of those men's branch.  In addition, those men's test results should provide insight into the order and time at which the major R1a1a Ashkenazi Levite lines branched off from one another.

Over the next several years, SNP testing is likely to continue to become less expensive, more comprehensive, and more popular. We have started to identify a relatively small number of SNPs that are of significance to R1a1a Ashkenazi Levites and their closest matches; identification of a comprehensive set of such SNPs will require the testing of a representative group of men who are farther from the mode.

The testing companies will likely tailor their comprehensive Y-DNA SNP testing to test for these SNPs by, for example, testing for them using chip-based genotyping (chip-based genotyping is considerably less expensive than next generation Y-DNA sequencing) to test for all Y-DNA SNPs identified through full Y-DNA sequencing; in the meantime, it should be possible to test SNPs of special interest on an a la carte basis.

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Click here for a schematic tree that shows the SNP test results received to date for R1a1a Ashkenazi Levites and their two closest matches who are not R1a1a Ashkenazi Levites.  Click here for a calculation of the time to calculations for the age of R1a1a Ashkenazi Levite subclades, as calculated by reference to SNPs.

Avrum Halevy Leiferman

Avrum Halevy Leiferman (@1840-1910)
Photograph taken @1890 in Kamenets-Podolsk, Ukraine