J-M410 subclades and clusters overview

Any discussions about this haplogroup

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Joined: Fri Mar 30, 2012 11:43 pm

YDNA:
J2a4b3
MtDNA:
L3d
PostPosted: Fri Apr 12, 2013 5:10 pm
ChrisR wrote:tree sub of M67 reconstructed by using Project and Geno2 data: J2a-M67-CTS3261_N62009_Ison, J2a-M67-CTS3261-YSC0000292_230305_Magamadov, J2a-M67-CTS3261-Z365_N10172_Anonychuk, J2a-M67-L210_252114_Berry, J2a-M67-L210_29875_Ross, J2a-M67-L210-Z482_51341_Lewkowicz, J2a-M67-L210-Z482_N32818_Friedman, J2a-M67-Z467_139708_Frank, J2a-M67-M92-PF7404_222662_Espino, J2a-M67-M92-Z515_174923_Miller, J2a-M67-Z500-PF7394_21636_Piotrowski

Image

ChrisR,
What a beautiful analysis! I had just realized a couple of days ago that the L210/L227 branch split off into Z492 and the more terminal SNP, Z482. Z482 likely characterizes the specific Ashkenazi L210/L227's while Z492 without Z482--Ross, Berry--will characterize the broader Z489s I have found across the Mediterranean eg Sicily, NW Turkey. Curiously, Z489 was dropped from the Geno 2.0 reporting in mid-stream, but I think it will be equivalent to Z492. So L227/L210 and Z492 are relatively recent--Late Bronze Age--Eastern Mediterranean and Aegean SNPs upon which Z482 occurred in an Ashkenazi or proto-Ashkenazi population.
Roy
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PostPosted: Fri Apr 12, 2013 5:31 pm
royking wrote:ChrisR,
What a beautiful analysis! I had just realized a couple of days ago that the L210/L227 branch split off into Z492 and the more terminal SNP, Z482. Z482 likely characterizes the specific Ashkenazi L210/L227's while Z492 without Z482--Ross, Berry--will characterize the broader Z489s I have found across the Mediterranean eg Sicily, NW Turkey. Curiously, Z489 was dropped from the Geno 2.0 reporting in mid-stream, but I think it will be equivalent to Z492. So L227/L210 and Z492 are relatively recent--Late Bronze Age--Eastern Mediterranean and Aegean SNPs upon which Z482 occurred in an Ashkenazi or proto-Ashkenazi population.
Roy

Thanks Roy. This is my first broader analysis in M67 clades and certainly I have to correct and add some more information. AngelaC and CharlesI have already helped in a first check. I have a M67+ M92- Alpine kit which is to be sent back to FTDNA. Will be interesting to find out the tree position.
DNA/Admixture Central Europe (Alps, Tyrol, Dolomites, Raetia); Y-DNA J2a-L1064, J2a-L210, R1a-M17, R1b-U106 (L48-); mtDNA J1b1b, J1c1d, U5a2b2, U5b1b1. Projects : J2-M172, J2a-PF5197, Alpine DNA, ISOGG Wiki
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PostPosted: Fri Apr 19, 2013 1:36 am
preview/unfinished f v1.4 Update April 2013 (waiting for confirmation):
a) new split below L26: N17486 is positive for PF5116, PF5125 and the following SNPs are not reported: PF5119, PF5123, PF5127, PF5138
b) PF4499+ is not reported in some samples: 51341 (L210), 23148 (L70), N17486 (P329.2) and also not in all J2b samples: N42743 => seems unreliable
c) N22333 of cluster *G defines a new clade sub of L26: F292
d) added new results kit N76290 (PF5160 > PF5169 > PF5177). By using 1000 Genomes comparison (NA20884, NA21090) further refining of probable clades.
e) Geno2 results for 229942 and confirmation by N113379: A1 is still L26*
f) 91610 (in *E PF5116+) is Z2227- Z2229-
g) by PGP141 sequence results (provided by JaG) the following SNP positions where rechecked: Z2394, L776, L777/YSC0000248, PF7421
h) 270132 under J2a-M410 is PF4610+ and (new) CTS10721+
i) 268280 is J2a-M319 (M319+ not detected by Geno 2.0 but by 23andMe) and CTS1489-
j) minor adjustments (acquivalents of L24 and M67, adding Cluster *J)
k) Geno2 results for N88317 add new split PF5174: PF5160 > PF5169 > (CTS3183.2). Many SNPs not reliable in this sample.

Image
DNA/Admixture Central Europe (Alps, Tyrol, Dolomites, Raetia); Y-DNA J2a-L1064, J2a-L210, R1a-M17, R1b-U106 (L48-); mtDNA J1b1b, J1c1d, U5a2b2, U5b1b1. Projects : J2-M172, J2a-PF5197, Alpine DNA, ISOGG Wiki

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Joined: Thu Apr 05, 2012 3:07 pm

YDNA:
j2a3d
PostPosted: Fri Apr 26, 2013 7:29 pm
f 1.4 version April 2013 point i
Kit 268280 (M319) is CTS1489-
However a closely related kit 94083 (M319) is CTS1489+

I'd welcome any comment
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PostPosted: Fri Apr 26, 2013 10:24 pm
horncastle wrote:f 1.4 version April 2013 point i
Kit 268280 (M319) is CTS1489-
However a closely related kit 94083 (M319) is CTS1489+

All the new Geno 2.0 SNPs are under investigation. This is especially valid for recurrent SNPs in a terminal place like CTS1489. As you can see in the link the SNP is already positive in many haplogroups and also diverse J-groups. Probably either Geno 2.0 can not test it reliably or it is not a unique enough SNP (more like a STR DYS-marker). So I fear we have to drop it and M319 and *I group members can not be diversified with Geno 2.0 test only.
DNA/Admixture Central Europe (Alps, Tyrol, Dolomites, Raetia); Y-DNA J2a-L1064, J2a-L210, R1a-M17, R1b-U106 (L48-); mtDNA J1b1b, J1c1d, U5a2b2, U5b1b1. Projects : J2-M172, J2a-PF5197, Alpine DNA, ISOGG Wiki
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PostPosted: Tue Apr 30, 2013 3:05 pm
Courtesy of LudmillaR the J2a-L24 tree with Geno 2.0 kits indicated:
http://image-upload.de/image/2ToCij/3486b62bb1.jpg
DNA/Admixture Central Europe (Alps, Tyrol, Dolomites, Raetia); Y-DNA J2a-L1064, J2a-L210, R1a-M17, R1b-U106 (L48-); mtDNA J1b1b, J1c1d, U5a2b2, U5b1b1. Projects : J2-M172, J2a-PF5197, Alpine DNA, ISOGG Wiki
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PostPosted: Mon Jun 10, 2013 2:31 pm
J2a-M410 (xL24,M67) Phylogeny research v1.5 preview c unfinished - June 2013 (waiting for confirmation):
a) new split below L26: N17486 is positive for PF5116, PF5125 and the following SNPs are not reported: PF5119, PF5123, PF5127, PF5138
b) PF4499+ is not reported in some samples: 51341 (L210), 23148 (L70), N17486 (P329.2) and also not in all J2b samples: N42743 => seems unreliable
c) N22333 of cluster *G defines a new clade sub of L26: F292
d) added new results kit N76290 (PF5160 > PF5169 > PF5177). By using 1000 Genomes comparison (NA20884, NA21090) further refining of probable clades.
e) Geno2 results for 229942 and confirmation by N113379: A1 is still L26*
f) 91610 (in *E PF5116+) is Z2227- Z2229-
g) by PGP141 sequence results (provided by JaG) the following SNP positions where rechecked: Z2394, L776, L777/YSC0000248, PF7421
h) 270132 under J2a-M410 is PF4610+ and (new) CTS10721+
i) 268280 is J2a-M319 (M319+ not detected by Geno 2.0 but by 23andMe) and CTS1489-
j) minor adjustments (acquivalents of L24 and M67, adding Cluster *J)
k) Geno2 results for N88317 Yedidia add new split PF5174: PF5160 > PF5169 > (CTS3183.2). Many SNPs not reliable in this sample.
l) 23417 Devoni establishes position of the big *C cluster and adds a split: PF5116 > PF5123* (PF5119 no read)
m) 261187 Al-HaSHemeY confirms and defines new L581 branch: PF5007,PF5050,PF7381 > L581? > PF5000,PF7384*
n) 248045 Varela adds new split (if no read errors): PF5160 > PF5169 > PF5199* (PF5174-?). PF5197 is not reported. L1064 by unpublic result moved under PF5169 branches.
o) inclusion of Geno 2.0 and public Y-sequence id numbers for better overview

See Google folder - direct link to PDF

Image
DNA/Admixture Central Europe (Alps, Tyrol, Dolomites, Raetia); Y-DNA J2a-L1064, J2a-L210, R1a-M17, R1b-U106 (L48-); mtDNA J1b1b, J1c1d, U5a2b2, U5b1b1. Projects : J2-M172, J2a-PF5197, Alpine DNA, ISOGG Wiki

Posts: 11
Joined: Thu Apr 05, 2012 3:07 pm

YDNA:
j2a3d
PostPosted: Thu Jun 13, 2013 11:15 pm
Hi Chris, thanks for this. Can you elaborate on the meaning of the blue line and entries below M319 that refer to Iberians and Peruvians.
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PostPosted: Fri Jun 14, 2013 1:08 am
horncastle wrote:Can you elaborate on the meaning of the blue line and entries below M319 that refer to Iberians and Peruvians.

This are two 1000 Genomes samples (public full sequences) positive for M319. By comparison with M67 sequences the SNPs Z2227 and Z2229 where found.
DNA/Admixture Central Europe (Alps, Tyrol, Dolomites, Raetia); Y-DNA J2a-L1064, J2a-L210, R1a-M17, R1b-U106 (L48-); mtDNA J1b1b, J1c1d, U5a2b2, U5b1b1. Projects : J2-M172, J2a-PF5197, Alpine DNA, ISOGG Wiki
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Posts: 269
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PostPosted: Sat Jul 13, 2013 2:43 am
HUGE UPDATE!!!
J2a-M410 (xL24,M67) Phylogeny research 1.6a

From analysis of many new (from this year) 1000 Genomes Y-sequences I got a more refined phylogeny. Luckily there where one M47 and three M67 samples. Guess their position before viewing the image, on M67 I had a thought now confirmed ;-)
Also single sequences in seldom lineages like PF4610* and PF5008* available now, but only in the following branches a SNP research trough comparison of more then one sample seems interesting: Z2227* (maybe Cluster *C?), PF5174*, YSC246

https://docs.google.com/file/d/0B9ajLqi ... d4Z08tZlU/

This update was done by doing further SNP research on the J2a (xL24,M67) samples listed by yfull.com/1000genomes (yfull.com/tree/J2a):
1) M47 is positive and under Z2227,PF5119 - see HG02490 PJL-Punjabi also L290+
2) M68 is not positive for PF5160/Z2221 or PF5116 - see HG03693 & HG03854 STU-Tamil and HG02651 PJL-Punjabi.
3) new basal haplogroup PF5008, PF5039, PF5050, PF5053 trough HG01589 PJL-Punjabi. Unfortunately L581 is not available in this sample.
3) L558 and Z1848 are confirmed as valid haplogroup above M67, M319 and Cluster *I: only roughly checked in M67 samples. Needs further investigation.
4) HG03018 & HG02724 PJL-Punjabi are Z2227,PF5119* and therefore candidates for Cluster *C. SNP investigation interesting.
5) HG02774 PJL-Punjabi confirms the PF4610 haplogroup and is probably a member of the *1 Clusters.
6) PF5174* assumed bigger size/distribution is confirmed by six! sequences positive for this clade: HG03905 & HG03012 BEB-Bengali, HG02733 & HG02493 PJL-Punjabi, HG04107 & HG04003 STU-Tamil. SNP investigation interesting.
7) YSC246 (YSC0000246) confirmed by HG03660 & HG03021 PJL-Punjabi. SNP investigation interesting.
8) YSC253 confirmed by HG03615 BEB-Bengali. PF4341 needs further investigation; maybe unreliable.
Last edited by ChrisR on Sun Jul 14, 2013 8:13 pm, edited 1 time in total.
DNA/Admixture Central Europe (Alps, Tyrol, Dolomites, Raetia); Y-DNA J2a-L1064, J2a-L210, R1a-M17, R1b-U106 (L48-); mtDNA J1b1b, J1c1d, U5a2b2, U5b1b1. Projects : J2-M172, J2a-PF5197, Alpine DNA, ISOGG Wiki
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