Revisiting the lineages of the Cohanim using data from next-generation sequencing

Background Early studies using a handful of Y-chromosome markers showed that many self-declared Jewish priests (Cohanim) share related haplotypes, but the limited resolution left open how many priestly lineages exist, when they arose, and how they map onto Jewish population history. Objectives We used whole-Y sequencing and modern phylogenetic tools to (i) catalogue Y-chromosome clades that are robustly enriched among Cohanim, (ii) date their most-recent common ancestors (TMRCAs) with pedigree-calibrated clocks, (iii) reconstruct their geographic dispersal across the Jewish Diaspora, and (iv) offer a stable, SNP-block nomenclature for future work. Methods We generated 104 new Big Y-700 sequences from rigorously documented Cohanim spanning 20 diaspora origins, and incorporated 215 legacy samples re-typed for diagnostic SNPs. Phylogenies and branch TMRCAs were built on the FTDNA and YFull backbones. A branch qualified as “Cohen” (CB) if ≥5 men and ≥50 % of branch members self-identified as Cohanim. Results Nine Cohen branches met these criteria, and for the current study were designated CB-01 to CB-09 with numbering based on antiquity of SNP-block coalescence. CB-01 is the largest (∼45 % of all Cohanim sampled), the most ancient (TMRCA ≈ 850 BCE), and the only lineage present in every major Jewish community. Its internal topology shows explosive branching between 700 and 300 BCE, stasis through the Roman-Byzantine era, and renewed expansion after 800 CE, mirroring known demographic pulses. CB-02 (TMRCA ≈ 700 BCE) and CB-03 (≈ 550 BCE) likewise trace to Iron- or late Classical-period Judea but are geographically narrower. CB-04 – CB-07 are Near-Eastern clades whose priestly status may have crystallized 0–1000 CE, while CB-05, CB-08 and CB-09 appear to derive from Mediterranean host populations. Twenty percent of Cohanim fall outside any current CB, indicating that additional, rarer lineages remain to be characterized. Conclusions High-resolution sequencing reveals a small set of divergent paternal lines comprising the Jewish priesthood, dominated by a pre-exilic Levantine lineage whose branch structure traces three millennia of geographically dispersed Jewish demographic history. The CB nomenclature, SNP catalogues and open dataset provided here supply a reproducible framework for genetic and historical studies which illustrate the broader power of dense uniparental phylogenies in population-genetic inference.