A few days after my previous post on the Cohen modal haplotype, here is an abstract from the October ASHG meeting which essentially confirms my main points, that the CMH is not indicative of Hebrew ancestry and is split between J1 and J2 lineages.
An Updated World-Wide Characterization of the Cohen Modal Haplotype.
J.E. Ekins et al.
Since the definition of the Cohen Modal Haplotype (CMH) in 1998, the 6 SNP-6 STR genetic motif has been utilized to infer connections of contemporary individuals and communities to the ancient Hebrew population. The elucidation of the YCC SNP Phylogeny has allowed cataloguing of chromosomes compatible with the original CMH definition into several different Y-SNP subclades. Haplogroup membership was determined for 266 samples matching at ≥5 of the CMH STR alleles, defined as the Cohen Modal Haplogroup (CMHg). The bulk of the CMHg chromosomes were observed in J1 (53.0%) and J2 (43.2%), with a small portion falling outside of haplogroup J (3.8%). Members of the CMHg were observed throughout the world, with significant frequencies in various Arab populations: Oman (20.1%), Iraq (15.2%), Palestine (9.5%). Coalescent simulations were performed for CMH chromosomes within each SNP haplogroup using 24 STR loci. Estimates within J1 [6.5kybp(4K-12K)] and J2 [13kybp(7K-27K)] were substantially deeper than previous figures obtained from a heavily weighted Jewish sampling, indicating a likely origin of the compound haplotype prior to the establishment of the Hebrew population. The significant presence of CMH chromosomes in deeply divergent clades J1 and J2 (>20kybp), indicates the present CMH definition is not sufficient to distinguish lineages that likely arose by parallel IBS mutations. An expanded STR definition is proposed which allows differentiation between CMH-compatible chromosomes in J1 and J2. The inference of Jewish ancestry based on the original CMH definition should be performed with caution as subjects may be falsely categorized into the eponymous CMH lineage when the true origin is in the deeply divergent IBS branch. These observations underscore the importance of using updated SNP classifications when utilizing the CMH to infer ancestry in Jewish populations, or the use of the expanded STR definition.