2013 Rootsi et al. Paper on Origins of R1a1a Ashkenazi Levites

The Paper and Its Findings
In short, Rootsi & Behar conclude, based upon the presence of the 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 identify six SNPs - including M582 - that are characteristic of R1a1a Ashkenazi Levites and their closest matches. (They identify 13 other SNPs that are found in R1a1a Ashkenazi Levites but not their closest matches.)

2. They report 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 identify 10 M582+ samples from Jewish men who are not Ashkenazi. They report 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 identify 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 note that this man "might represent the legacy of Jews or Moors in Iberia."

5. They identify 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 identify M582 in only one of 211 R1a1a men sampled in the Caucasus.

6. They state 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 note that "[t]he higher R1a-M582 diversities and frequencies observed among Near Eastern populations indicate R1a-M582 originated in this geographic region." They conclude 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 estimate 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 includes a table identifying SNPs, by loci, for the men for whom they obtained full Y-DNA sequencing results.
That figure identifies, 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 identifies 13 SNPs that were found in both of the Ashkenazi samples but not in the Iberian sample.  (Note that these SNPs are listed according to the numerical order of their loci; further data is needed to determine the order in which SNP mutations occurred.) Finally, the figure identifies 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 report 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 report 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 has identified one of the SNPs identified as having been found in  "Ashkenazi Jew P3" but not "Ashkenazi Levite 16207" as Y2630/S4574. 
Further Analysis
Full Genomes Corp. has done full Y-DNA testing of Jamal Kussad, who is Z2122+ F1345+ CTS6-.  That testing shows that Kussad is positive on one of the six SNPs identified by Rootsi & Behar - F2997 - but negative on the remaining five SNPs.  That means that: (1) M582/CTS2253/ Z2474 is at the same level as F1345 (not reported in Supplementary Figure 1 to the Rootsi & Behar et al. paper), at least until an R1a1a man is found with one SNP but not the other; and (2) F2997 is upstream from (a) Z2469/CTS6, (b) M582/CTS2253/Z2474, (c) Z2475/CTS3412, (d) Z2476/CTS3605, and (e) Z2477/CTS8448.

Click here for a discussion of the SNPs identified by Rootsi & Behar that have been found in more than one R1a1a Ashkenazi Levite; the page attaches a schematic tree showing which men have those SNPs and other SNPs that have been found in more than one R1a1a Ashkenazi Levite.
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