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Sunday, December 29, 2013

Globe13 Calculator for genetic distance, biogeographical ancestry, and Oracle

Today, I am presenting a quite big Excel file (93 MB) that I generated to calculate genetic distances, biogeographical ancestry, and Oracle.
The file can be found in Data Sink.
Here is the direct link.

How to use it:
1. Open file in Excel; enable Macro.
2. Go to sheet "Paste here!" and add your Globe13 component values in cells B2 - N2.
3. Go to "Tools", then "Macro", then run Macro "Sort".
4. You are done. The results appear on sheet "Paste here!". Based on your computer the calculations can take up to one minute.

Example: results for Kurd_D

1. Top100 matches for Kurd_D (all samples)
 2. Top100 matches for Kurd_D (reference populations only)
3. Oracle TOP500 combinations for Kurd_D (reference populations only)
4. OracleTOP500 combinations for Kurd_D (all samples)
5. Predicted location for biogeographical ancestry of Kurd_D

The calculated latitude and longitude numbers can be directly pasted into

Previously, I used this Excel file to generate some phylogenetic trees and a map.

Wednesday, December 18, 2013

Ashkenazi-Levite Jews and their Iranian origin Part II

Previously, I mentioned that I believe that the term "Ashkenazi" is ultimately derived from the Iranian name "Ashkan", the founder of the Parthian Empire (still called 'Ashkanian' (اشکانیان) Empire in Iranian languages).

I already showed that the Ashkenazi Jews share a lot genetic markers with Kurds:
  • mtDNA HV1b2 was found within Ashkenazi Jews and one Yezidi Kurd;
  • the Y-haplogroup of the Kurd N91920 is J1c3 and he shares the SNP L817+ with the J1c3* Jewish Cluster A. Thus, the closest and the only Middle Eastern relative of the J1c3* Jewish Cluster A is a  Kurdish individual.    
  • The R1a1a Ashkenazi-Levite cluster shows similarities to the STR data of a Kurdish individual.

A new publication in Nature comes to the same conclusions about the R1a-M582 Ashkenazi-Levite cluster, it is not East European, it is not Khazarian, it is Iranian.

From the paper:

Phylogenetic applications of whole Y-chromosome sequences and the Near Eastern origin of Ashkenazi Levites

Considering the historical records of Ashkenazi Jews, three potential geographic sources should be considered: the Near East, which was the geographic location for the ancient Hebrews; Europe, which was the residence of the Ashkenazi Jewish Diaspora and the region in which they evolved for nearly two millennia; and the region overlapping with the no longer extant mid-11th Century Khazarian Khaganate, whose ruling class has been suggested to have converted to Judaism18. Our data render the latter source highly unlikely since the Khazarian Khaganate overlapped with the Northern Pontic-Caspian steppe and the North Caucasus region, in which just one Nogay sample carried the R1a-M582 haplogroup (Table 1). Furthermore, the Nogays, formerly a powerful Kipchak Turkic-speaking nomadic confederation, are relatively recent inhabitants of the Caucasus, and the STR haplotype of the sole R1a-M582 Nogay sample lies outside of the Levite cluster. Had the Caucasus region been the source for the Ashkenazi modal lineage, we likely would have found R1a-M582 Y-chromosomes in some of its 20 local populations examined in our sample of more than 2,000 Y-chromosomes (Table 1). As previously suggested, the European and particularly, the Eastern European paternal gene pool was seen as a natural and highly plausible source for the Ashkenazi Levite lineage as both the Ashkenazi community and haplogroup R1a frequencies peak in this region. But surprisingly, haplogroup R1a-M582 was not detected in non-Jewish Eastern European samples and was found only in singleton samples in various Central and Western European populations (Table 1).
Near Eastern populations are the only populations in which haplogroup R1a-M582 was found at significant frequencies (Table 1). Moreover, the representative samples displayed substantial diversity even within this geographic region (Fig. 1b). Higher frequencies and diversities often suggest lineage autochthony. Hence, we can assess whether or not the origin of haplogroup R1a-M582 is in present-day Iran and eastern Anatolia, or rather the broader region of the Near East. Our data demonstrate the occurrence of R1a-M582 among different Iranian populations, among Kurds from Cilician Anatolia and Kazakhstan, and among Ashkenazi and non-Ashkenazi Jews. These observations, and the STR network delineating an internal R1a-M582 structure, might attest to a broad Near Eastern distribution range of this minor haplogroup that survived to the present day at low frequencies among Iranian Kerman, Iranian Azeri, Kurds and Jews. Haplogroup R1a-M582 was not detected in samples from Iraq or among Bedouins, Druze and Palestinians sampled in Israel.

One thing the paper did not address well is to highlight the frequency of R1a-M582 within R1a1 individuals of each population. From all tested non-Jewish population Kurds have the highest frequency of R1a-M582 within R1a1 individuals. Caution, the number of tested R1a individuals is pretty low, so percentages might be off.

Here is the ranking based on the data of the publication:

100% (2/2) Jews from Israel (Non-Ashkenazi)
100% (2/2) Jews from Algeria (Non-Ashkenazi)
100% (2/2) Jews from Slovenia (Non-Ashkenazi)
92% (80/87) Ashkenazi Jews* 
73% (90/123) Jews
67% (6/9) Jews from Spanish Exile (Non-Ashkenazi)
67% (2/3) Jews from Bulgaria (Non-Ashkenazi)
50% (2/4) Jews from Turkey (Non-Ashkenazi)
43% (3/7) Kurds (Turkey and Kazakhstan)
40% (2/5) Jews from North Africa (Non-Ashkenazi)
29% (2/7) Jews from Near East (Non-Ashkenazi)
28% (10/36) Non-Ashkenazi Jews 
19% (9/48) Iran (Azeri)
13% (3/24) Iran (Kerman)
10% (2/21) Iran
9% (1/11) Nogays 
6% (18/303) Near East
6% (1/17) Iran
5% (1/21) Hungary
2% (1/42) Germany 
1% (1/106) Western/Northern Europe 
1% (1/119) Slovakia 
1% (22/2711) Non-Jewish populations