Prepublication of Y phylogenies by G. Magoon and al-2013


Posts: 143
Joined: Sun Mar 18, 2012 6:26 pm
Location: Paris region
YDNA:
G2a2b2a1b1a2a-CT4803
MtDNA:
H2a2a1 (rCRS)
PostPosted: Mon Dec 23, 2013 10:11 am
In the newsletter of the haplogroup G, Ray Banks said "In our prepublication paper involving 1000 Genomes Project samples and a few other samples, "
http://biorxiv.org/content/biorxiv/earl ... 2.full.pdf

The figure 1 is a cladogram overview of the automatic-constructed demonstration tree based on 1292-sample dataset.

In this overview, BT branches off from A1b-T and B and CT branches off from BT. nothing new for this part of the cladogram.

There is a paragraph for haplogroup B :

"In haplogroup B, the seven diverse samples included in the 1000 Genomes Project, from the Gambia (1) , Sierra Leone (2 in Mende ethnic group) , Kenya (3 in Luhya ethnic group) and Puerto Rico (1) allow the discovery of significant new structure at the root of the haplogroup. Three of the samples, HG02588, HG03225 and HG03376, along with the four other haplogroup B samples, share derived results at 38 SNPs, including M60, M181, and V244, which define the haplogroup in the ISOGG and other published trees.
But these three samples are ancestral for two SNPs which were formerly thought to define haplogroup B, P90 and M247/P85. They are also ancestral for the SNPs that define both of the known B subgroups, B1 and B2, as shown in Table 4.

These three samples’ results allow a new B3 clade to be recognized alongside B1 and B2, the members of which share novel derived SNP results at over 800 mutation sites (Z5057-Z5852) not derived in any other samples -- the large number reflecting the great age of haplogroup B. Interestingly, these three 1000 Genomes Project samples
also share nine more derived SNPs (L1388-L1394, L1396, and L1397), of the eleven new mutations found in the 352,776 bp tested in a 2013 “Walk Through the Y” participant from the Bahamas, another member of this clade.

Within the new B3 branch, a subclade can also be defined by the over 200 derived SNPs (Z11473- Z11671) which the two Mende samples have in common.
"

It is to compare to the ISOGG tree http://www.isogg.org/tree/ISOGG_HapgrpB.html

B M60, M181/Page32, M247/P85, P90
• B* -
• B1
• • B1* -
• • B1a
• B2
• • B2* -
• • B2a
.....................................................................................................................
• • B2b
.....................................................................................................................

Posts: 143
Joined: Sun Mar 18, 2012 6:26 pm
Location: Paris region
YDNA:
G2a2b2a1b1a2a-CT4803
MtDNA:
H2a2a1 (rCRS)
PostPosted: Mon Dec 23, 2013 11:28 am
We have 4 figures about the numbers of SNPs

1) The members of B haplogroup "share derived results at 38 SNPs "
2) the members of new B3 (2 Mende and 1 Gambian) share over 800 mutation sites not derived in any other samples"
3) The members of new B3 "also share nine more derived SNPs .... found in a 2013 WTY participant from the Bahamas, another member of this clade."

If we try to evaluate the elapsed time between the fork of CT/B and the fork of the 2 subclades (2 Mende versus 1 Gambian) of B3 with over 38+800+9=847 mutations, We don't know the average number of years/mutation for the 1000 GP and this new method of exploration of raw data, but if we take :

- 1 mutation every 75 years, we have got over 847x75 = 63,525 years
- 1 mutation every 100 years, we have got over 847x100 = 84,700 years
- 1 mutation every 125 years, we have got over 847x125 = 105,875years

4) "Within the new B3 branch, ..... over 200 derived SNPSs common to the two Mende samples"

- 1 mutation every 75 years, we have got over 200x75 = 15,000 years
- 1 mutation every 100 years, we have got over 200x100 = 20,000 years
- 1 mutation every 125 years, we have got over 200x125 = 25,000 years

Therefore, between the birth of the B branch and the TMRCA of the 2 Mende of Sierra Leone we have got

- 1 mutation every 75 years, we have got over 78,525 years
- 1 mutation every 100 years, we have got over 104,700 years
- 1 mutation every 125 years, we have got over 130,875 years

We can think the TMRCA of the 2 Mende is below 20,000 years old certainly and probably a lot less. Admittedly 10,000 years very roughly, we have got from the birth of B .

- 1 mutation every 75 years, about 88,000 years
- 1 mutation every 100 years, about 115,000 years
- 1 mutation every 125 years, about 140,000 years

We can think the birth of B (with the divergence of CT branch) dates of about the "Out of Africa" event and I think the "Out of Africa" is dating of the Eemian in the beginning of the first phase MIS5e (130-120,000BP) of the interglacial, the best estimation for these testings is 1 mutation every 115 years, about 130,000 years ago for the birth of haplogroup B.

You are allowed to have an other opinion !

Posts: 143
Joined: Sun Mar 18, 2012 6:26 pm
Location: Paris region
YDNA:
G2a2b2a1b1a2a-CT4803
MtDNA:
H2a2a1 (rCRS)
PostPosted: Mon Jan 06, 2014 12:43 pm
Poznik et al-2013 started of a first colonization of America at the end of LGM, about 15,000 years ago,for the calibration, although this datation of the event is strongly contestated with strong archeological evedesnces seemingly.
"In a separate study on page 562, Poznik et al. (2) detail their methods using sequences from 69 males drawn from nine populations, covering 9.99 million loci on the Y, and conclude that the most recent common paternal ancestor lived 120,000 to 156,000 years ago. "

Poznik et al. d find an average mutation rate of 0,82x10-9/bp-1/year-1 (0,72-0,92 10-9 range ). for 9,99M this gives about 1 mutation every 122 years.

If we compare the tree in the paper of Poznik and al-2013 by taking the bifurcation of Y-haplogroups of F, G, H, IJ K (with Mt hgs M, N) in the warm Odderade phase of the 'Out Of Arabia' population of South Asia as far as Sunda (West Indonesia) and South China 86-74,000 years ago, I obtain an average mutation rate of about 1 mutation every 180years. Therefore average mutation rate of 0,55x10-9/bp-1/year-1 very close to 0,53x10-9/bp-1/year-1 from Francalacci et al-2013

If I am dating by 1 mutation every 180 years, I obtain

- Separation of A1 and BT : about 212,000 years ago (near the birth of Mts L1 and L2'3'4'5'6)

- Separation of B and CT : about 155,000 years ago (near the birth of Mts L2 and L3'4'6) . This would precede an "Out Of Africa of 130-125,000 years, while no CT sub-branches (except E branch are greatly found in African and it seems E was born in Arabia). But maybe, CT was born in North-East Africa in the beginning of the Nubian Culture before 130,000BP, a lineage migrated to Arabia/Near East about 130,000BP and the other remaining lineages disappeared in Africa, maybe with the comeback of E into Africa after 115,000BP. I remind a lot of archeological traces of the Nubian Culture were found in Arabia from about 110-100,000 years and moderbskulls found in Near East from 115,000-90,000 (things a lot of geneticiens refused to consider, preferring the lower and politically more correct date of 70-55,000BP (and this ancient date only because there were forced by the datation of the arrival date of modern humans in Sahul (Australia and New Guinea) more than 50,000 years by Australian scientifics), but they have continued refusing an arrival into America before LGM against the more evident archeological and linguistic clues).

- Separation of B2a and B2b : about 105,000 years ago .

- Separation of DE and CF : about 115,000 years ago (near the birth of Mts L3 and L4) .

- Separation of E1b1a and E1b1b: about 75-70,000 years ago .

- Separation of F, G, H, IJ and K : about 88-80,000 years ago (near the birth of Mts M and N) .

- Separation of K, LT, MP, NO : about 82-75,000 years ago (near the birth of Mt R) .

- Separation of N and O : about 75-70,000 years ago . A the beginning (very contrasting between 75 ,00BP and 68,000BP) of the first pleniglacial phase

- Separation of P and Q : about 59-55,000 years ago . After the end of the first pleniglacial phase (59,000BP)

- Separation of Q-L54 and Q-M3 : about 40-35,000 years ago, maybe a little later (35-30,000) as the tree length is shorter. As Q-M3 was probably born in America, the arrival of the haplogroup Q-L54 (with Mt hg C1,D1 and X2, Mt hg A and B arrived later) into America should be dated of the warmer Arcy oscillation (34-33000BP) in the same time R1b and Gravettian Culture entered into Europe from Russia. It is possible the first arrival of the Modern Human (Australoid type) was sooner about 55,000BP with Y-hg C3* and Mt-hg D1 (it remains to analyse the rare South American C3* to know their separation date with the Asian and North American C3), I don't dare to imagine before the first pleniglacial about 77-70,000BP in the time of the Toda Volcano explosion (73,000BP) .
Last edited by palamede on Tue Jan 28, 2014 12:52 pm, edited 4 times in total.

Posts: 2231
Joined: Fri Mar 16, 2012 5:43 pm

MtDNA:
U5b2b
PostPosted: Wed Jan 15, 2014 3:18 pm
I think that your TMRCAs for all the haplogroups are the only realistic ones that I have seen yet.

Posts: 2231
Joined: Fri Mar 16, 2012 5:43 pm

MtDNA:
U5b2b
PostPosted: Thu Jan 23, 2014 7:56 pm
I saw a post at anthrogenica about the variance of I being five times that of R. If that is right and the Siberian R was dated to 24,000 ybp wouldnt that put the I haplogroup in the 120,000 year range?

Posts: 143
Joined: Sun Mar 18, 2012 6:26 pm
Location: Paris region
YDNA:
G2a2b2a1b1a2a-CT4803
MtDNA:
H2a2a1 (rCRS)
PostPosted: Fri Jan 24, 2014 12:36 pm
dartraighe wrote:I saw a post at anthrogenica about the variance of I being five times that of R. If that is right and the Siberian R was dated to 24,000 ybp wouldnt that put the I haplogroup in the 120,000 year range?


The sentence was from "Alan", he said
"I think for me the simple logic that dawned on me was Ken calculated I to have about 5 times as much variance as western European R1b and because he dated I at the time to around 20000BC or something like that then there was no way R1b could be anywhere near the sort of 30000BC date that was once popular - that would create a nonsense age of 150,000 years for I in relative terms. ".

I don't know if it is right, I am surprised by the magnitude 5. It would need to be verified.

For the divergence from the splitting of the 2 big branches I1 and I2, Ken Nordtvedt dated to around 20,000BC.

With 1 mutation every 200 years (8,9Mbp, low coverage), I found The phylogenic tree of Francalacci et al.-2013 gives
- a splitting of K and IJ about 90,000-85,000BP,
- a splitting of I and J 80,000-75,000BP (a long time before what I guessed (About 50,000BP)),
- a splitting of I1 and I2 (50,000-60,000BP, therefore before Europe entry, something surprising)
- a splitting of I2a, I2b, I2c (50,000-40,000BP) during first expansion in Anatolia and Europa)
- a splitting of I2a1a (Spain) and I2a1b (Pannonic basin) (about 40,000BP) maybe during Aurignacian expansion in Europa).

It is about 55,000BP instead of 22000BP, 2,5 times more . When the number of samples in every branches are unequal, we know the estimated divergence is pulled towards the divergence of the more numerous branche(s). In this case we can suppose the egality was almost perfect and there is no bias. if we admit the splitting of I1 and I2 is 55,000BP but we don't know to describe the shape of the coalescence (demographic development of sub-branches) of the I branches and it is very imprtant for the estimated divergence? birth is

If it i,s allowec to take the magnitude 5 for the ages but I am far to be certain of the validity, the beginnning of the coalescence of western European R1b (and not Siberian R) would be about 11000BP , about the time of the end of the last cold maximum of the Younger Dryas dated to about 11,500BP which is a time of population expansion in Europe, specially toward Britanic Isles, North Europa and East Europa. it is also the time of the last big explosion of the Phlegraean_Fields "Approximately 12,000 years ago the last major eruption occurred, forming a smaller caldera inside the main one, centered on the town of Pozzuoli.", but we don't know the demographic consequence in Italy and South Europe.

It is not impossible first ancestry of West European dating to about 30,000BP and the divergence correponds to a coalesccence time of 11,000 years, all these is depending to the demographic expansion rate with the encountered bottlenecks.

To validate West European R1b paleolithic hypotheses , downstairs of R1b-L11, it will be mandatory to find at least more than 100 SNPs for 10Mbp (Big Y) and more than 140 SNPs for 14Mbp (Full Genomics). Now, I guess FGC has found about 60-80 confirmed SNPs for numerous testees, which not yet enough for Paleolithic hypothesis (140-200), but already a few too many for Indo-European hypothesis.

Posts: 2231
Joined: Fri Mar 16, 2012 5:43 pm

MtDNA:
U5b2b
PostPosted: Fri Jan 24, 2014 2:01 pm
Palamede
thanks for taking time to answer my question.

Return to B Haplogroup (Y-DNA)

Who is online

Users browsing this forum: No registered users and 1 guest