Tuesday, February 11, 2014

Ethiopian YDNA J STR Analysis - An addendum

In the past, I had carried out a TMRCA (STR) analysis of YDNA haplogroup J haplotypes from Ethiopia using the primary dataset from the Plaster thesis that was discussed here. While that particular dataset had a large number of haplotypes, it also had a low number of Markers (6). However there was supplementary data that had Y-STR Haplotypes from haplogroup J supplied with the paper. While it only had data for a select few of the populations found in the main paper, it however had better resolution typing at 14 markers. Below are the TMRCA results for those haplotypes. The Dataset can be found in this table in .csv format under "Ethiopian_JM267.csv".
In total, 54 haplotypes were found in the supplementary dataset, nevertheless the total number of haplotypes among the population groups sum up to 53 above, the reason is because one haplotype that belonged to the Anuak dataset was not included.

The results are quite consistent with the results I got from the dataset with less resolution, even if the sample sizes are quite small. For instance, although the Afar had the J Haplogroup in excess of 25%, their haplotypes show the least amount of diversity, conversely the high diversity of Haplogroup J in the other populations is still maintained. 

While the Zhivotovsky TMRCA (Z-TMRCA) for all the 691 YDNA J haplotypes found in Ethiopia in the lower resolution dataset was previously calculated to 595 generations, the Z-TMRCA for the higher resolution dataset for all 54 haplotypes, as seen above, was calculated to 705 generations, if only the markers that were used in the lower resolution data set were used to compute the Z-TMRCA in these 54 haplotypes we would get a Z-TMRCA of 631 Generations. Furthermore, if we intersected the 14 markers from this dataset with the recommended Zhivotovsky markers, the resulting markers of '19', '393', '392', '391', '390', '439', '388', '389-1' and '389-2' , would yield a Z-TMRCA of 920 generations, implicating  an introduction of YDNA J-M267 in Ethiopia well into the Upper Paleolithic.

Update: With respect to the low resolution haplotypes from the plaster thesis; I have added 5,726 YDNA str haplotypes  in *.csv format compatible with the calculator and tabulated according to the UEPs tested, in the Table at this link below as well: http://ehelix.pythonanywhere.com/init/default/Example_Files

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