Note: A major reorganization has occurred in J2 per a recent article by Sengupta et al. There are conflicting models in the subclades under J2b (M12) from Semino's and Sengupta's studies which have not yet been fully resolved.

J   12f2.1, M304, S6, S34, S35
�       J*   -
�       J1   M267
�      �       J1*   -
�      �       J1a   M62
�      �       J1b   M365
�      �       J1c   M367, M368
�      �       J1d   M369
�      �       J1e   M390
�       J2   M172
�      �       J2*   -
�      �       J2a   M410
�      �       �       J2a*   -
�      �       �       J2a1    DYS413≤18
�      �       �      �       J2a1*   -
�      �       �      �       J2a1a   M47, M322   (formerly J2a)
�      �       �      �       J2a1b   M67/S51   (formerly J2f)
�      �       �      �       �       J2a1b*   -
�      �       �      �       �       J2a1b1   M92, M260   (formerly a part of J2f1)
�      �       �      �       �      �       J2a1b1*   -   
�      �       �      �       �      �       J2a1b1a   M327    (formerly a part of J2f1)
�      �       �      �       �       J2a1b2   M163, M166    (formerly J2f2)
�      �       �      �       J2a1c   M68    (formerly J2b)
�      �       �      �       J2a1d   M137    (formerly J2c)
�      �       �      �       J2a1e   M158    (formerly J2d)
�      �       �      �       J2a1f   M289
�      �       �      �       J2a1g   M318    (formerly J2k)
�      �       �      �       J2a1h   M319    (formerly J2l)
�      �       �      �       J2a1i   M339    (formerly J2g)
�      �       �      �       J2a1j   M419
�      �       �      �       J2a1k    DYS445≤7 (formerly known as J2x)
�      �       �       J2a2   M340    (formerly J2h)
�      �       J2b   M12, M314, M221    (formerly J2e)
�      �       �       J2b*   -
�      �       �       J2b1   M102     (formerly J2e1)
�      �       �      �       J2b1*   -   
�      �       �      �       J2b1a   M241    (formerly J2e1b)
�      �       �      �       �       J2b1a*   -
�      �       �      �       �       J2b1a1   M99    (formerly J2e1a)
�      �       �      �       �       J2b1a2   M280    (formerly J2e1c)
�      �       �      �       �       J2b1a3   M321    (formerly J2e1b1)
�      �       �      �       J2b1b   M205    (formerly J2e2, then J2b2)

• In J2a1b the designation M67/S51 means that these two SNPs are identical but were discovered separately. The listing is alphabetical, not necessarily in the order of discovery.
S51 is positive in one individual. It was hypothesized that the placement of this snp would be J2a1b3 until it was found that S51 was equivalent to M67 (J2a1b).
• M12/M102 is reported as J2b and M410 is reported as J2a in Sengupta et al (2006) while Regueiro gives M12/M102 as J2a and M410 as J2b. We are using the Sengupta interpretation.

Y-DNA haplogroup J evolved in the ancient Near East and was carried into North Africa, Europe, Central Asia, Pakistan and India. J2 lineages originated in the area known as the Fertile Crescent. The main spread of J2 into the Mediterranean area is thought to have coincided with the expansion of agricultural peoples during the Neolithic period. The timing of the demographic events that brought J2 to Central Asia, Pakistan, and India is not yet known. J1 lineages may have a more southern origin, as they are more often found in the Levant region, other parts of the Near East, and North Africa, with a sparse distribution in the southern Mediterranean flank of Europe, and in Ethiopia.

There is a descending gradient in the frequency of occurrence of haplogroup J from the Middle East toward the northwest of Europe, reaching about 3% of the population on the northwest Atlantic coast. The occurrence of J in Europe is undoubtedly due both to the Neolithic expansion and to episodic migrations, though the relative proportion of those two sources is controversial and may not be the same in different locations.

A significant fraction of Jews belong to haplogroup J, but Jews represent a small minority of the European members of the haplogroup. The "Cohen Modal Haplotype" is a specific set of six Y-STR marker values that occurs in both J1 and J2, though at a much higher frequency in J1. It is likely that those of Cohanim descent and carrying the CMH belong to the J1 haplogroup, though more study is needed.

References:

Alonso et al, The Place of the Basques in the European Y-chromosome Diversity Landscape. (available by subscription) European Journal of Human Genetics, 13:1293-1302, 2005.
Behar et al, Contrasting Patterns of Y Chromosome Variation in Ashkenazi Jewish and Host Non-Jewish European Populations. (pdf) Hum Genet 114:354-365, 2004.
Capelli et al, Population Structure in the Mediterranean Basin: A Y Chromosome Perspective. (pdf) Annals of Human Genetics, 2005.
Cinnioglu et al, Excavating Y-chromosome Haplotype Strata in Anatolia. (pdf) Human Genetics. 114:127-148, 2004.
Cruciani et al, A Back Migration from Asia to Sub-Saharan Africa Is Supported by High-Resolution Analysis of Human Y-Chromosome Haplotypes. (pdf) American Journal of Human Genetics, 70:1197-1214, 2002.
Cruciani et al, Tracing Past Human Male Movements in Northern/Eastern Africa and Western Eurasia: New Clues from Y-Chromosomal Haplogroups E-M78 and J-M12. (pdf) Molecular Biology and Evolution 24(6):1300-1311, 2007.
Di Giacomo et al, Y Chromosomal Haplogroup J as a Signature of the Post-Neolithic Colonization of Europe. (pdf) Human Genetics, 115:357-371, 2004.
Flores et al, Reduced Genetic Structure of the Iberian Peninsula Revealed by Y-chromosome Analysis: Implications for Population Demography. (available by subscription) European Journal of Human Genetics, 12:855-863, 2004.
Karafet et al, Paternal Population History of East Asia: Sources, Patterns, and Microevolutionary Processes. (pdf) American Journal of Human Genetics, 69:615-628, 2001.
Kivisild et al, The Genetic Heritage of the Earliest Settlers Persists in Both Indian Tribal and Caste Populations. (pdf) American Journal of Human Genetics, 72:313-332, 2003.
Myers et al, (2007), Y-chromosome Short Tandem Repeat DYS458.2 Non-concensus Alleles Occur Independently in Both Binary Haplogroups J1-M267 and R1b3-M405. Croatian Medical Journal, 48, 2007.
Nasidze et al, MtDNA and Y-chromosome Variation in Kurdish Groups. (abstract) Annals of Human Genetics, 69:401-412, 2005.
Regueiro et al, Iran: Tricontinental Nexus for Y-Chromosome Driven Migration. (abstract) Human Heredity, Vol. 61, No 3, 132-143, 2006.
Semino et al, Ethiopians and Khoisan Share the Deepest Clades of the Human Y-Chromosome Phylogeny. (pdf) American Journal of Human Genetics, 70:265-268, 2002.
Semino et al, Origin, Diffusion, and Differentiation of Y-Chromosome Haplogroups E and J: Inferences on the Neolithization of Europe and Later Migratory Events in the Mediterranean Area. (pdf) American Journal of Human Genetics, 74:1023-1034, 2004.
Sengupta et al, Polarity and Temporality of High Resolution Y-chromosome Distributions in India Identify Both Indigenous and Exogenous Expansions and Reveal Minor Genetic Influence of Central Asian Pastoralists. (pdf) American Journal of Human Genetics, 78:202-221, 2006.
Shen et al, Reconstruction of Patrilineages and Matrilineages of Samaritans and other Israeli Populations from Y-Chromosome and Mitochondrial DNA Sequence Variation. (pdf) Human Mutation, 24:248-260, 2004.

Additional Resources:

Dennis Garvey, Y Haplogroup J
Andreas O., The M410 Project
Bonnie Schrack and Jeff Schweitzer, The Y-Haplogroup J DNA Project
Ron Scott, J2: Frequency Distribution of Extended Haplotypes Gathered from YSearch
Costa Tsirigakis, J2 Y DNA group

Corrections/Additions made since 20 December 2006:

• Added Ron Scott reference in Additional Resources on 8 June 2007.
• Added Cruciani et al (2007) on 17 June 2007.
• Rewrote first note in Notes on 17 October 2007.
• Added Myers et al (2007) on 17 October 2007.

Contact People for Haplogroup J: Bonnie Schrack or Whit Athey

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