Minimal reference J2 phylogeny

The makers of the mtDNA reference phylogeny (Mannis van Oven, et al.) did setup a “minimal reference” for the Y-DNA haplogroups. Team members are in contact with Mannis to achieve an updated and optimized J2-M172 minimal reference: . Primary goals of

[…] optimal global discrimination capacity based on a strongly reduced set that includes only the most resolving Y-SNPs. […]
(iii) Y-SNPs defining terminal haplogroups that have an (expected) regional population frequency of at least 2%, as determined from a population sample consisting of at least 50 unrelated males sampled in a geographic area spanning at least 100 km.
(iv) All Y-SNPs included in the reference tree need to be observed in at least five patrilineally unrelated males who do not have their genealogical origin in the same village. In this way, ‘private’ mutations that are specific to single families are avoided.

Minimal reference phylogeny for the human Y chromosome
van Oven M, Van Geystelen A, Kayser M, Decorte R, Larmuseau MH. 2013. Seeing the wood for the trees: a minimal reference phylogeny for the human Y chromosome. Hum Mutat (in press). doi:10.1002/humu.22468

Updated version 8-Nov-13
Includes important new branches in J2a: PF5197, YSC253, PF5172, Z6065. M47 and L198 are now omitted.

Updated version 1-Dec-2013
updates in the basic skeleton, rs-numbers added

Primary typing SNPs with phylo-equivalent alternatives shown in parentheses. Recurrent SNPs are indicated with a # suffix.

J2 M172=rs2032604 (L228=rs371968167) J-M172*(xM410,M12)
J2a M410=rs371079691 (L559=rs373707621) J-M410*(xL26,L581)
L26=rs34459399 J-L26*(xZ2221,Z2227,M68)
Z2221 (Z2220) J-Z2221*(xM530,PF5197)
M530=rs35248080 J-M530*(xM158,L25)
M158=rs375691065 J-M158
L25=rs34534058 J-L25*(xF3133,PF4888,Z387)
F3133 J-F3133
PF4888 (PF5401) J-PF4888
Z387 J-Z387
PF5197 J-PF5197*(xYSC253,PF5172)
YSC253 J-YSC253
PF5172 J-PF5172
Z2227=rs367734743 (Z2229=rs376384057 PF5116=rs374310420 Z1848=rs376572995) J-Z2227*(xZ6065,M67,M319)
Z6065 J-Z6065
M67=rs2032628 J-M67*(xPF5132,Z467)
PF5132 J-PF5132*(xM92,PF7394)
M92=rs2032648 J-M92
PF7394 J-PF7394
Z467=rs369454960 J-Z467*(xL227)
L227 (L210) J-L227
M319=rs13447373 J-M319
M68 J-M68
L581 J-L581
J2b M12=rs3903 (M102=rs2032608 L282=rs377565422) J-M12*(xM205,M241)
M205=rs2032657 J-M205
M241=rs8179022 J-M241*(xL283,Z2432)
L283 J-L283
Z2432 J-Z2432

About Chris Rоttensteiner

Chris Rоttensteiner. Population Genetics: Phylo-Genetics & Haplogroups, Population Admixture & History, Family and Genetic Genealogy, South Tyrol, Alps, Central Europe.