age of main J-M304 nodes (J1, J2, J2a, J2b) haplogroup

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PostPosted: Thu Oct 16, 2014 2:31 am
Collection of some useful discussions and assumptions for years/SNP/bp estimates:
  • 2013-11 Michał mutation rate of 0.7 10^-9 per nucleotide per year, 0.82 - 0.53, as proposed by Poznik and Francalacci
    63.0 (53.7-82.8) haplogroup F
    61.9 (52.8-81.3) haplogroup IJK
    58.8 (50.1-77.3) haplogroup K
    40.2 (34.3-52.9) haplogroup P
  • 2014-01 Michał mutation rate of 0.66 x 10^-9 per nucleotide per year
    38.8 (40.2, 38.5) haplogroup P
    1 SNP in the “gold region” (of about 10 Mb) covered by the FTDNA Big Y test should correspond to about 151 years/SNP BigY
  • 2014-04 Michał 180 years/SNP BigY when not counting additional SNPs that are seen in the VCF file only or are extracted from the BAM file (only on the number of reliable HQ variants reported by FTDNA) because the range of Big Y is actually slightly larger than 10 Mb.
  • 2014-05 Michał Big Y test covers approximately 60% of all SNPs tested by FGC, which would correspond to 91 years/SNP for FGC
  • 2014-05 Iain McDonald used Big Y results for four relatively large and deeply rooted families (three R1b and one R1a) with known genealogies to estimate that each reliable BigY-tested SNP (i.e. an SNP mutation verified by the analysis of the vcf files) corresponds to about 140 years/SNP BigY, with a 95.5% confidence level of 104-197 years/SNP. Corresponds to 84-81 years/SNP FGC.
  • 2014-10 Iain McDonald thread about U106 ages with 132.7 years/SNP BigY (95% CI 102.8 -173.7), 136.7 years/SNP literature (CI 120.1 - 156.7), 136.1 years/SNP literature+BigY (CI 119.8 -155.8). Adjustment for the age distribution of the Big-Y testers was applied.

Possible calibration points to verify any estimate:
  • CDEF-M168 age (modern Y expansion to Eurasia), majority thinks could be not older then approx. 70,000 years
  • IJ-M429 age (modern Y expansion to Europe) should be not younger then oldest homo sapiens evidence in Europe approx. 43,000 years ago
  • Q-sublineages only present in America (Q1a3a1-L54(xM3), modern Y expansion to America), not older then oldest homo sapiens evidence in America believed to be not older then approx. 18,000 years ago (LGM)
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: Thu Oct 23, 2014 12:52 am
I forgot to mention ancient Y-DNA sequences as calibration points, some examples where a Y-sequence is available AFAIK:
  • 43,000 BC: Siberian (Ust'-Ishim) K(xLT)
  • 22,000 BC: Siberian Mal'ta R(xR1,R2)
  • 5,780-980 BC: Hungarians KO1 I2a, NE5+NE6 C6, NE7 I2a, BR2 J2a-Y3021(xY3612), IR1 N
  • 3,300 BC: Ötzi the Iceman together with one South German FGC Y-Elite: G2a2a1a2a1a-FGC5672

EDIT: estimates from the Ust'-Ishim paper:
- CDEF-M168 (no B) - 72 (+-9) kya
- IJK (no other F) - 54 (+-5) kya
- C-M130 (Dai_B is C2, others C1) - 53 (+-8) kya
- E-M96 (both E1 and E2 samples) - 53 (+-8) kya
- K2 (no LT) - 50 (+-4) kya
- IJ - 49 (+-6) kya


So as said here, CDEF-M168 almost surely needs to have happened before 65 ky and IJ seems almost 50ky old.
Last edited by ChrisR on Sat Nov 08, 2014 8:02 pm, edited 3 times 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

Posts: 2154
Joined: Fri Mar 16, 2012 5:43 pm

MtDNA:
U5b2b
PostPosted: Thu Oct 23, 2014 9:10 am
ChrisR wrote:Collection of some useful discussions and assumptions for years/SNP/bp estimates:
  • 2013-11 Michał mutation rate of 0.7 10^-9 per nucleotide per year, 0.82 - 0.53, as proposed by Poznik and Francalacci
    63.0 (53.7-82.8) haplogroup F
    61.9 (52.8-81.3) haplogroup IJK
    58.8 (50.1-77.3) haplogroup K
    40.2 (34.3-52.9) haplogroup P
  • 2014-01 Michał mutation rate of 0.66 x 10^-9 per nucleotide per year
    38.8 (40.2, 38.5) haplogroup P
    1 SNP in the “gold region” (of about 10 Mb) covered by the FTDNA Big Y test should correspond to about 151 years/SNP BigY
  • 2014-04 Michał 180 years/SNP BigY when not counting additional SNPs that are seen in the VCF file only or are extracted from the BAM file (only on the number of reliable HQ variants reported by FTDNA) because the range of Big Y is actually slightly larger than 10 Mb.
  • 2014-05 Michał Big Y test covers approximately 60% of all SNPs tested by FGC, which would correspond to 91 years/SNP for FGC
  • 2014-05 Iain McDonald used Big Y results for four relatively large and deeply rooted families (three R1b and one R1a) with known genealogies to estimate that each reliable BigY-tested SNP (i.e. an SNP mutation verified by the analysis of the vcf files) corresponds to about 140 years/SNP BigY, with a 95.5% confidence level of 104-197 years/SNP. Corresponds to 84-81 years/SNP FGC.
  • 2014-10 Iain McDonald thread about U106 ages with 132.7 years/SNP BigY (95% CI 102.8 -173.7), 136.7 years/SNP literature (CI 120.1 - 156.7), 136.1 years/SNP literature+BigY (CI 119.8 -155.8). Adjustment for the age distribution of the Big-Y testers was applied.


Possible calibration points to verify any estimate:
  • CDEF-M168 age (modern Y expansion to Eurasia), majority thinks could be not older then approx. 70,000 years
  • IJ-M429 age (modern Y expansion to Europe) should be not younger then oldest homo sapiens evidence in Europe approx. 43,000 years ago
  • Q-sublineages only present in America (Q1a3a1-L54(xM3), modern Y expansion to America), not older then oldest homo sapiens evidence in America believed to be not older then approx. 18,000 years ago (LGM)



Some U106 testers have more SNPs downstream from their terminal SNP than others. In my group some have 40 SNPs so I think that they should divide the number into the estimated age of the subgroup to find the average years per SNP for their own specific Y-lines.
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PostPosted: Mon Nov 10, 2014 4:53 pm
New estimates recalibrated on Ust'-Ishim paper:
CDEF-M168 (no B) - 72 (+-9) kya
IJK (no other F) - 54 (+-5) kya
IJ - 49 (+-6) kya

using the last IJ estimate:
J 36
J2 33
J2a 24
J2a-PF4610 21
J2a-L26 19
J2a-Z2227 16
J2a-L558 15
J2a-M67 14
J2a-L24 14
J2a-L25 9
J2a-PF5174 11 (not sure if all diversity is included)
J2b 18 (not sure if all diversity is included)
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: 587
Joined: Thu Mar 15, 2012 11:59 am

YDNA:
Adam-L74; R1a-YP4700
MtDNA:
H14a
PostPosted: Sun Nov 30, 2014 6:13 pm
In this diagram IJ is a bit earlier, equal to K-M9

Image
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PostPosted: Mon Dec 01, 2014 12:55 am
Atim wrote:In this diagram IJ is a bit earlier, equal to K-M9

Interesting diagram of the R1a-M417 lineages Hg ages, but I only see IJK-M523 and K-M9 ages. The ages of the "fraternal pairs" are not included.
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: 286
Joined: Mon Apr 23, 2012 6:15 pm
PostPosted: Sun Feb 15, 2015 10:43 am
First version of Age estimates by YFull (J2 subhaplogroups in the latest ISOGG draft version):
http://www.yfull.com/tree/CT/
CT-M168 formed 76500 ybp, TMRCA 68200 ybp
CF-P143 formed 68200 ybp, TMRCA 65300 ybp
F-M89 formed 65300 ybp, TMRCA 49200 ybp
GHIJK-M3658 formed 49200 ybp, TMRCA 49200 ybp
HIJK-M578 formed 49200 ybp, TMRCA 47900 ybp
IJK-L15 formed 47900 ybp, TMRCA 46700 ybp
IJ-M429 formed 46700 ybp, TMRCA 42800 ybp
I-M170 formed 42800 ybp, TMRCA 27500 ybp
I1-M253 formed 27500 ybp, TMRCA 4900 ybp
I2-M438 formed 27500 ybp, TMRCA 21300 ybp

http://www.yfull.com/tree/J/
J-M304 formed 42800 ybp, TMRCA 31300 ybp
J1-M267 sformed 31300 ybp, TMRCA 18800 ybp
J2-M172 formed 31300 ybp, TMRCA 27700 ybp
J2a-M410 formed 27700 ybp, TMRCA 17800 ybp
J2a1-PF4610 formed 17800 ybp, TMRCA 16200 ybp
J2a1a-L26 formed 16200 ybp, TMRCA 16200 ybp
J2a1a1-PF5087 formed 16200 ybp, TMRCA 16200 ybp
J2a1a1a-Z2221 formed 16200 ybp, TMRCA 15800 ybp
J2a1a1a1-L24 formed 15800 ybp, TMRCA 13600 ybp
J2a1a1a1a-L25 formed 13600 ybp, TMRCA 9500 ybp
J2a1a1a1a1-Z387 formed 9200 ybp, TMRCA 5000 ybp
J2a1a1a1a1a-L70 formed 5000 ybp, TMRCA 4500 ybp
J2a1a1a1a1a3-CTS6061 formed 4200 ybp, TMRCA 3200 ybp
J2a1a1a2-PF5197 formed 15800 ybp, TMRCA 15400 ybp
J2a1a1a2a-YSC0000253 formed 15400 ybp, TMRCA 9900 ybp
J2a1a1a2a1-YSC0000246 formed 9900 ybp, TMRCA
J2a1a1a2b1-PF5169 (incl. PF5171) formed 13000/12800 ybp, TMRCA 11200 ybp
J2a1a1a2b1c-PF5174 formed 11200 ybp, TMRCA 8400 ybp
J2a1a1b-PF5125 formed 16200 ybp, TMRCA 16200 ybp
J2a1a1b1-Z2227 formed 16200 ybp, TMRCA 14500 ybp
J2a1a1b1a-L558 formed 14500 ybp, TMRCA 14500 ybp
J2a1a1b1a1-M67 formed 14500 ybp, TMRCA 12700 ybp
J2a1a1b1a1a1-L210 formed 12700 ybp, TMRCA 5000 ybp
J2a1a1b1a1b-PF5132 formed 12700 ybp, TMRCA 11400 ybp
J2a1a1b1a1b1-M92 formed 11400 ybp, TMRCA 8200 ybp
J2a1a1b1a1b1b-CTS2906 formed 8200 ybp, TMRCA 6400 ybp
J2a1a1b1a1c1-CTS900 formed 12000 ybp, TMRCA 8700 ybp
J2a1a1b1a1c1a-CTS6804 formed 8700 ybp, TMRCA 7500 ybp
J2a1a1b1a2-Z2243 formed 14500 ybp, TMRCA 13500 ybp
J2a1a1b1a2a-M319 formed 13500 ybp, TMRCA 12700 ybp
J2a1a1b1b-Z6065 formed 14500 ybp, TMRCA 13700 ybp
J2a1a2-Z6059 formed 16200 ybp, TMRCA 9800 ybp
J2a1a2a-Z6056 formed 9800 ybp, TMRCA 8900 ybp
J2a2-PF5008 formed 17800 ybp, TMRCA 16400 ybp
J2b-M12 formed 27700 ybp, TMRCA 18100 ybp
J2b1a-M241 formed 13300 ybp, TMRCA 9700 ybp
J2b1a1-L283 formed 9700 ybp, TMRCA 8500 ybp
J2b1a1a1a1-Z631 formed 3500 ybp, TMRCA 2700 ybp

R-M207 formed 31600 ybp, TMRCA 27800 ybp
R1-M173 formed 27800 ybp, TMRCA 22400 ybp

Compare TMRCA estimates of Nov 10, 2014 estimates with YFull in kya:
CT 72 vs 68
IJK 54 vs 47
IJ 49 vs 43
J 36 vs 31
J2 33 vs 28
J2a 24 vs 18
J2a-PF4610 21 vs 16
J2a-L26 19 vs 16
J2a-Z2227 16 vs 15
J2a-L558 15 vs 15
J2a-M67 14 vs 13
J2a-L24 14 vs 14
J2a-L25 9 vs 10
J2b 18 vs 18

The basal nodes seem estimated a bit younger by YFull while the more recent clades seem to almost coincide.
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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