Dan Graur's Latest Bombshell and Implications for Jewish Genetics

** The Oldest Y Chromosome that Wasn’t ** from Dan Graur

Yesterday Eran Elhaik and Dan Graur of ENCODE- fame published another ‘investigative science’ paper with two other colleagues, where they showed that a recent sensational discovery by Michael F. Hammer’s group was full of flaws and statistical biases. Their finding has major implications for population genetic studies on Jews, because most major claims in that field, including those on origin of priestly families, came from Hammer and colleagues.

How many of those need to be revised or debunked? We asked Dr. Elhaik about that and other implications of his paper. Please note that he is one of our ‘Best of 2013’ judges, and we also covered his research work on Jewish genetics in earlier commentaries.

New Study Sheds Light on the Origin of the European Jewish Population

Population Genetics Study on Khazar Origin of Jews is Back in Spotlight

Haldane’s Sieve blog covered the same issue in April 2013. Please check here for insightful discussion.

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Q1. Why did you suspect in the first place that there was something wrong in their analysis? Were you just curious, or did you encounter their data through other work?

Upon first reading, I was puzzled by the peculiar comparison of chromosomes of uneven sizes and the use of autosomal data to calculate the mutation rate for the Y chromosome. It wasn’t until I was asked to refute the paper that I reviewed it more rigorously. When I began to believe that the results were manipulated, I asked my colleagues to join the research effort.

Q2. Did you have problem getting the paper accepted in a journal, or did it get accepted at the first place you sent to?

Not unexpectedly, the first journal we approached rejected the manuscript on the ground that it doesnt fit the journal. The paper was accepted to EJHG whose reviewers also helped pointing out additional problems with the Mendez et al. (2013) paper.

Q3. Does Hammer and colleagues know about your analysis? What has been their response so far?

Absolutely.Some of the authors of the original paperwere instrumental inthe preparation of our paper and one of them was acknowledged for his contribution. We also asked some of the authors to comment on the manuscript prior to submission and accepted all their comments.

Q4. What are the likely counterclaims about your analysis?

Only counterclaims that are common to papers in the field, such as the accuracy of the Y chromosomal mutation rate and whether it changed over time.

Q5. Do you have suspicion that other results by the same group are similarly exaggerated?

While I am not familiar with all the studies of this group,a plain search in the literature would reveal that some of the authors ofthe Mendez et al. (2013) paperhave previouslyreported the Cohanim modal haplotype [1,2], Levite modal haplotype [3,4], and the so-called Jewish genome[5] - all of which have been challenged on similar grounds including but not limited to applying unsuitable methods [6,7], using incorrect mutation rates6, data manipulation [6,8-10], and other alleged attempts to manipulate the results [6,11]. The study about the Jewish genome and origin of European Jews was challenged by myself [12].

Q6. Based on your analysis, do the statistical errors appear to be intentional (purposely done to make inflated claim), or are they likely to be honest mistakes?

I cannot speak to intent, however random errors arelikelyto both inflate and deflate the chromosome age and this is not what weobserved.

1. Skorecki, K. et al. Y chromosomes of Jewish priests. Nature 385, 32, doi:10.1038/385032a0 (1997).

2. Thomas, M. G. et al. Y chromosomes traveling south: the cohen modal haplotype and the origins of the Lemba–the “Black Jews of Southern Africa”. Am. J. Hum. Genet. 66, 674-686, doi:S0002-9297(07)63439-9 [pii] 10.1086/302749 (2000).

3. Behar, D. M. et al. Multiple origins of Ashkenazi Levites: Y chromosome evidence for both Near Eastern and European ancestries. Am. J. Hum. Genet. 73, 768-779, doi:S0002-9297(07)63626-X [pii] 10.1086/378506 (2003).

4. Thomas, M. G. et al. Origins of Old Testament priests. Nature 394, 138-140, doi:10.1038/28083 (1998).

5. Behar, D. M. et al. The genome-wide structure of the Jewish people. Nature 466, 238-242, doi:nature09103 [pii] 10.1038/nature09103 (2010).

6. Klyosov, A. A. A comment on the paper: Extended Y chromosome haplotypes resolve multiple and unique lineages of the Jewish Priesthood by M.F. Hammer, D.M. Behar, T.M. Karafet, F.L. Mendez, B. Hallmark, T. Erez, L.A. Zhivotovsky, S. Rosset, K. Skorecki, Hum Genet, published online 8 August 2009. Hum. Genet. 126, 719-724; author reply 725-716, doi:10.1007/s00439-009-0739-1 (2009).

7. Tofanelli, S. et al. J1-M267 Y lineage marks climate-driven pre-historical human displacements. Eur. J. Hum. Genet. 17, 1520-1524, doi:10.1038/ejhg.2009.58 (2009).

8. Zoossmann-Diskin, A. Are today’s Jewish priests descended from the old ones. Homo 51, 156-162 (2000).

9. Zoossmann-Diskin, A. et al. Protein electrophoretic markers in Israel: compilation of data and genetic affinities. Ann. Hum. Biol. 29, 142-175, doi:10.1080/03014460110058971 (2002).

10. Zoossmann-Diskin, A. Ashkenazi levites’ “Y modal haplotype” (LMH) - an artificially created phenomenon? HOMO - Journal of Comparative Human Biology 57, 87-100 (2006).

11. Levy-Coffman, E. A mosaic of people: the Jewish story and a reassessment of the DNA evidence. J. Genetic Genealogy 1, 12-33 (2005).

12. Elhaik, E. The Missing Link of Jewish European Ancestry: Contrasting the Rhineland and the Khazarian Hypotheses. Genome Biology and Evolution 5, 61-74, doi:10.1093/gbe/evs119 (2013).