2013 Rootsi et al. Paper on Origins of R1a Ashkenazi Levites

On December 17, 2013, Siiri Rootsi, Doron M. Behar, and their colleagues published a paper on R1a1a Ashkenazi Levites. S. Rootsi & D. Behar, et al., Phylogenetic Applications of Whole Y-Chromosome Sequences and the Near Eastern Origin of Ashkenazi Levites, Nature Communications 4, Article No. 2928 (2013). (Elsewhere on this website, R1a1a Ashkenazi Levites are referred to as R1a-Y2619 Ashkenazi Levites; for historical reasons, this page will use the term R1a1a Ashkenazi Levites to refer to men in that Y-DNA cluster.) 

Note that Dr. Behar’s November 2017 paper on R1a1a Ashkenazi Levites, D. Behar et al., The genetic variation in the R1a clade among the Ashkenazi Levites’ Y chromosome, SREP-17-37687 (2017), summarized here, confirms and expands upon the findings of the 2013 Rootsi & Behar paper on R1a1a Ashkenazi Levites

The Paper and Its Findings
 
In short, Rootsi & Behar concluded, based upon the presence of the Y-DNA SNP M582 in Ashkenazi Levites, Levites from non-Ashkenazi populations descended from Sephardim, and Near Eastern populations, that R1a1a Ashkenazi Levites likely originate in the Near East, rather than Khazaria or Europe.

Here are some of their most significant findings, in more detail:

1. They identified six SNPs - including M582 - that are characteristic of R1a1a Ashkenazi Levites and their closest matches. (They identified 13 other SNPs that are found in R1a1a Ashkenazi Levites but not their closest matches.)

2. They reported that M582 (aso known as CTS2253 and Z2474) was present in all sampled R1a1a Ashkenazi Levites, as well as 33.8% of other R1a1a Ashkenazi Jewish males and 5.9% of sampled R1a Near Eastern males.

3. They identified 10 M582+ samples from Jewish men who are not Ashkenazi. They reported that "[o]f the 10 non-Ashkenazi R1a-M582 individuals, two were from the North African Algerian community, six belonged to Spanish expulsion descendent communities of Slovenia, Turkey and Bulgaria, and two were from individuals reporting their last known parental origin as Israel." Eight of these men identified themselves as Levites; caste information was unavailable for the two men from Bulgaria.

4. They identified an Iberian man from the 1,000 Genomes database (designated in that database as HG01617, an Iberian sample) who shares six of the 19 SNPs that they found to be characteristic of R1a1a Ashkenazi Levites; one of the SNPs that he shares is M582. They noted that this man "might represent the legacy of Jews or Moors in Iberia."

5. They identified M582 in various R1a1a populations, "with the highest frequency occurring within Iranians collected from the southeastern Kerman population who self-identified as Persians, northwestern Iranian Azeri, and in Cilician Anatolian Kurds, at 2.86%, 2.50% and 2.83%, respectively." They identified M582 in only one of 211 R1a1a men sampled in the Caucasus.

6. They stated that "the previously proposed Eastern European origin of this lineage is no longer tenable given that our data suggest haplogroup R1a-M582 actually originated in the Near East." They noted that "[t]he higher R1a-M582 diversities and frequencies observed among Near Eastern populations indicate R1a-M582 originated in this geographic region." They concluded that, "the current data are indicative of a geographic source of the Levite founder lineage in the Near East and its likely presence among pre-Diaspora Hebrews," that "haplogroup R1a-M582 was likely carried into Europe by Jewish migrants and that it expanded among Ashkenazi Levites during their subsequent Diaspora period."

7. They provisionally estimated that the MRCA of R1a1a Ashkenazi Levites lived 1,500 to 2,500 years ago.

Specific SNPs Shared by R1a1a Ashkenazi Levites and Other M582+ Men
 
Supplementary Figure 1 to the Rootsi & Behar et al. paper included a table identifying SNPs, by loci, for the men for whom they obtained full Y-DNA sequencing results.
 
That figure identified, below Z2122, six SNPs that were found both in two Ashkenazi samples (one identified as "Ashkenazi Levite 16207" and one identified as "Ashkenazi Jew P3") and in an Iberian sample (identified as "Iberian HG01617"). That figure also identified 13 SNPs that were found in both of the Ashkenazi samples but not in the Iberian sample. Finally, the figure identified seven SNPs that are found in "Ashkenazi Levite 16207" but not "Ashkenazi Jew P3," and 14 SNPs that are present in "Ashkenazi Jew P3" but not "Ashkenazi Levite 16207."
 
Vladimir Tagankin, who runs the Semargl Y-DNA website, has prepared and posted an annotated table identifying most of these SNPs by name. (In a prior e-mail, Tagankin identified the SNPs designated with an S prefix as alternative names for certain SNPs appearing in his table, so the alternative names are added here.)
 
The six SNPs that Rootsi & Behar reported as having been found in both Ashkenazi samples and the Iberian sample are: (1) Z2469/CTS6; (2) M582/CTS2253/Z2474; (3) Z2475/CTS3412; (4) Z2476/CTS3605; (5) Z2477/CTS8448; and (6) F2997.
 
The 13 SNPs that Rootsi & Behar reported as having been found in both Ashkenazi samples but not the Iberian sample are: (1) Y2619/S4589; (2) Z2471; (3) Y2620/S4583; (4) Y2621; (5) Y2622/S4575; (6) Y2623; (7) Y2624/S4598; (8) Y2625/S4586; (9) Y2626; (10) an SNP, with the loci 18735386, for which Tagankin did not identify a name; (11) Y2627; (12) Y2628); and (13) Y2629. (Tagankin's table identifies two issues with this list: (1) Z2471 is present in the Iberian sample (HG01617) as well as the Ashkenazi samples, so it should be included with the six SNPs identified as being common to all three samples; and (2) the man identified as "Ashkenazi Jew P3" is negative for the SNP with the loci 18735386, so that SNP should be identified as private to "Ashenazi Levite 16207.")  
 
Tagankin identified one of the SNPs identified as having been found in "Ashkenazi Jew P3" but not "Ashkenazi Levite 16207" as Y2630/S4574.  

Further Discussions re the Paper
 
For further analysis and discussion of this paper, see the following:
 

Anatoly Klyosov's January 30, 2014 blog Поговорим о ДНК-генеалогии евреев, posted on pereformat.ru and translated here