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 www.phylotree.org/Y/:

[…] 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=rs34459399J-L26*(xZ2221,Z2227,M68)
 Z2221  (Z2220)J-Z2221*(xM530,PF5197)
 M530=rs35248080J-M530*(xM158,L25)
 M158=rs375691065J-M158
 L25=rs34534058J-L25*(xF3133,PF4888,Z387)
 F3133J-F3133
 PF4888  (PF5401)J-PF4888
 Z387J-Z387
 PF5197J-PF5197*(xYSC253,PF5172)
 YSC253J-YSC253
 PF5172J-PF5172
 Z2227=rs367734743  (Z2229=rs376384057  PF5116=rs374310420  Z1848=rs376572995)J-Z2227*(xZ6065,M67,M319)
 Z6065J-Z6065
 M67=rs2032628J-M67*(xPF5132,Z467)
 PF5132J-PF5132*(xM92,PF7394)
 M92=rs2032648J-M92
 PF7394J-PF7394
 Z467=rs369454960J-Z467*(xL227)
 L227  (L210)J-L227
 M319=rs13447373J-M319
 M68J-M68
 L581J-L581
J2b M12=rs3903  (M102=rs2032608  L282=rs377565422)J-M12*(xM205,M241)
 M205=rs2032657J-M205
 M241=rs8179022J-M241*(xL283,Z2432)
 L283J-L283
 Z2432J-Z2432

About Chris Rоttensteiner

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