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Maliclavelli
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« Reply #25 on: August 01, 2012, 01:44:16 PM »

SNPs in one sample did not give a good result!
The samples are 2 and not related. When it has been seen a relation father/son it has been said, and we don't know if the samples are closely or far related.
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Jean M
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« Reply #26 on: August 01, 2012, 01:47:27 PM »

Does the incorporation of these very upstream forms of R1b  haplotype among Jews in so many locations (Azkenazi and Sephardic??) implies it was around in some pre-European dispersal location in the middle east.  

I'm assuming that. Did you see the paper on the Cohanim? J1c3 (P58) is found in nearly half of the men who report themselves members of the hereditary Jewish priesthood (Cohanim). Other haplogroups found in the Cohanim include J2a (M410), J2b (M12), J2a3h2a1c (M318), R1b1a2 (M269) and E1b1b1b2a (M123), all found in the Near East.

 M. F. Hammer, Extended Y chromosome haplotypes resolve multiple and unique lineages of the Jewish priesthood, Human Genetics, vol. 126 (2009), pp. 707–717.
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JeanL
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« Reply #27 on: August 01, 2012, 01:50:08 PM »

@Stan

Would you mind explaining how you arrived to the conclusion that one SNP event can be estimated as occurring every 628 years?

I gotta admit, I'm rather confused by the methodology that Dienekes is using. I know Karafet.et.al.2008 did an interpolation methodology, where  the age of CT was fixed at 70 kya, and based on how downstream each SNP was with respect to CT, the age was calculated.

What I know is that the paternal germ-line autosomal mutation rates are much faster than maternal germ-line rates. Also, the mutation rate used by Dienekes was 3*10-8 mutations/nucleotide/generation. The y-chromosome has about 56 millions nucleotides, of course, I'm not sure how big the NRY section is, in terms of nucleotides, but most of the Y-chromosome is non-recombinant. So like I said before, I would greatly appreciate it, if you could explain how you came to the 628 years/SNP conclusion.

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Maliclavelli
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« Reply #28 on: August 01, 2012, 01:54:18 PM »

got to say the project Dienekes links through to

http://www.familytreedna.com/public/r1b1asterisk/default.aspx?section=ysnp

for very upstream R1b does look dominated y Jewish names.  I am not sure what that means in terms of very deep roots of R1b as the Jewish history is one of constant upheaval and movement.  Is there evidence for where and when the Jewish people picked up these upstream forms of R1b? I have never really looked much at these forms of R1b.  

I have studied these samples from many years. It is a constant that many Jewish haplotypes or clusters have a MRCA not more than 1000 years ago. This is explained by who believes to a Jewish ancestry by a bottleneck, by who doesn’t believe in it by an introgression.
If the haplogroup were Jewish before than 2000 years ago, we don’t understand why we don’t find some Jews related to this with mutations.
On the other hand the R1b1* (note: those with YCAII=18-23: the others, Eastern, with 23-23 or 21-23 have nothing to do with the European subclades) found in Europe (Iberia, Isles, Italy) have many mutations and belong to many different haplotypes.
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Maliclavelli


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vineviz
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« Reply #29 on: August 01, 2012, 04:44:56 PM »

Does the incorpotation of these very upstream forms of R1b  haplotype among Jews in so many locations (Azkenazi and Sephardic??) implies it was around in some pre-European dispersal location in the middle east.   

That is the most reasonable inference.
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« Reply #30 on: August 01, 2012, 04:52:07 PM »

got to say the project Dienekes links through to

http://www.familytreedna.com/public/r1b1asterisk/default.aspx?section=ysnp

for very upstream R1b does look dominated y Jewish names.  I am not sure what that means in terms of very deep roots of R1b as the Jewish history is one of constant upheaval and movement.  Is there evidence for where and when the Jewish people picked up these upstream forms of R1b? I have never really looked much at these forms of R1b.  
There are also some rarer forms of U152 and U106 that seem to have a little more correlation with the Jewish projects.

I speculated about this some time ago but I suspect that we'll have to come to grips with where R1b became a part of this group. Was it in the Near East or in the Rhine Valley? (which either could align with some accounts.) EDIT: ... well, it could be both and I suppose I should add in Italy although I'm not sure why.

EDIT: I see VV was thinking the same (the "both" part.)
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vineviz
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« Reply #31 on: August 01, 2012, 05:01:37 PM »

There are also some rarer forms of U152 and U106 that seem to have a little more correlation with the Jewish projects.

I speculated about this some time ago but I suspect that we'll have to come to grips with where R1b became a part of this group. Was it in the Near East or in the Rhine Valley? (which either could align with some accounts.)
Or both.

Some R1b chromosomes were likely in Jewish populations per-diaspora while others were likely introduced post-diaspora.

I'd put most R-M343(xL11) in the former and most R-L11 in the latter.
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Mike Walsh
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« Reply #32 on: August 01, 2012, 05:26:09 PM »

There are also some rarer forms of U152 and U106 that seem to have a little more correlation with the Jewish projects.

I speculated about this some time ago but I suspect that we'll have to come to grips with where R1b became a part of this group. Was it in the Near East or in the Rhine Valley? (which either could align with some accounts.)
Or both.

Some R1b chromosomes were likely in Jewish populations per-diaspora while others were likely introduced post-diaspora.

I'd put most R-M343(xL11) in the former and most R-L11 in the latter.

I'm not presenting any of these possibilities as my favorite or one as better than another, but here are some historical considerations.

1. The Jewish faith has a long tradition of Near East origin so that alternative probably doesn't need a lot of explanation.

2. The link up of Jewish migrations to/from the Rhine Valley.
Quote from: Wikipedia
"The Jews of Ashkenaz", are the Jews descended from the medieval Jewish communities along the Rhine in Germany from Alsace in the south to the Rhineland in the north.

I'll throw in another which is interesting for people who are intrigued by a PIE homeland.

3.  The Khazars of the Pontic Steppes had some number of Jewish immigrants and there are reports that many people of Khazaria converted to Judaism.
Quote from: Wikipedia
In 529, Prince Khosrau I of the Persian Empire fought the social movement led by the Zoroastrian priest Mazdak. Numerous Jewish families who supported the movement had to flee the country north of Caucasus Mountains...

Jewish communities had existed in the Greek cities of the Black Sea coast since late classical times. Chersonesos, Sudak, Kerch and other Crimean cities sustained Jewish communities, as did Gorgippia, and Samkarsh / Tmutarakan was said to have had a Jewish majority as early as the 670s. Jews fled from Byzantium to Khazaria as a consequence of persecution under Heraclius, Justinian II, Leo III, and Romanos I. These were joined by other Jews fleeing from Sassanid Persia (particularly during the Mazdak revolts), and, later, the Islamic world. Jewish merchants such as the Radhanites regularly traded in Khazar territory, and may have wielded significant economic and political influence. Though their origins and history are somewhat unclear, the Mountain Jews also lived in or near Khazar territory and may have been allied with the Khazars, or subject to them; it is conceivable that they, too, played a role in Khazar conversion

If one or more of these alternatives can be clearly ruled out as an origin for R1b found among Jews that would be clarifying.
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Maliclavelli
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« Reply #33 on: August 01, 2012, 06:47:27 PM »

I have said also recently that general theories should derive from single case studied and resolved.
The Italian-American Joe Merante have a tradition in his family of Jewish extraction:
1)   his Y is R-M269 with YCAII=17-23, diffused above all in Italy (only one case I found on SMGF and put on ySearch: the Lebanese Jlelaty)
2)   his mtDNA is J1b1b1. His FGS matches perfectly a Buryat and is close to other people of the same people. What do you think about it? That his maternal line was really Jewish one, but probably from a Khazar converted, seen that Khazars have the same origin of the Turkish Buryats. Recently a Jew, whose aunt is a Jewess coming from Turkey, asked me about her mtDNA: J1b1b1. I answered him the same. Recently a complete match in HVRI has been found in the Italian Alps, and this sincerely made me desire other investigations, but an origin from some Turk tribes during the migrations of people is likable, seen that there is in the Alps also 1 hg. M.
3)   Certainly a contribute of the Khazars to the Jewish pool is likable: someone thinks to Y G2c, R1a1a, probably some Q etc
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Maliclavelli


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alan trowel hands.
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« Reply #34 on: August 01, 2012, 06:52:16 PM »

I must admitt my understanding of Jewish history is practically zero but how far back was the time when the Ashkenazi and Sepharidic Jews parted ways and where was it?  Did they part company in the near east or do they have a more recent common ancestor?  I just ask because I (possibly in my ignornance) assume that the FTDNA list Dienekes linked to included both Ashkenazi and Sephardic sounding people.
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Humanist
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« Reply #35 on: August 01, 2012, 06:54:34 PM »

There are also some rarer forms of U152 and U106 that seem to have a little more correlation with the Jewish projects.

I speculated about this some time ago but I suspect that we'll have to come to grips with where R1b became a part of this group. Was it in the Near East or in the Rhine Valley? (which either could align with some accounts.)
Or both.

Some R1b chromosomes were likely in Jewish populations per-diaspora while others were likely introduced post-diaspora.

I'd put most R-M343(xL11) in the former and most R-L11 in the latter.

I'm not presenting any of these possibilities as my favorite or one as better than another, but here are some historical considerations.

1. The Jewish faith has a long tradition of Near East origin...

2. The link up of Jewish migrations to/from the Rhine Valley...

I'll throw in another which is interesting for people who are intrigued by a PIE homeland.

3.  The Khazars of the Pontic Steppes...

If one or more of these alternatives can be clearly ruled out as an origin for R1b found among Jews that would be clarifying.

Alternatives #2 and #3 can likely be ruled out for the Jewish R-L584 men.
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« Reply #36 on: August 01, 2012, 07:01:30 PM »

For one of the Cohanim R-L584 lines.  

Marko Heinila's tree data:

Quote
Assyrian #1, kit # 205749: TMRCA of 1848 years with Askhenazi Cohanim and Syrian Jewish men.

Assyrian #2, kit # 213562: TMRCA of 2239 years with Assyrian #1 and Askhenazi Cohanim and Syrian Jewish men. Another 1011 years (3250 years), connects him to four men.  One of the men lists France as an origin.
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Richard Rocca
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« Reply #37 on: August 01, 2012, 07:51:14 PM »

got to say the project Dienekes links through to

http://www.familytreedna.com/public/r1b1asterisk/default.aspx?section=ysnp

for very upstream R1b does look dominated y Jewish names.  I am not sure what that means in terms of very deep roots of R1b as the Jewish history is one of constant upheaval and movement.  Is there evidence for where and when the Jewish people picked up these upstream forms of R1b? I have never really looked much at these forms of R1b.  
There are also some rarer forms of U152 and U106 that seem to have a little more correlation with the Jewish projects.

I speculated about this some time ago but I suspect that we'll have to come to grips with where R1b became a part of this group. Was it in the Near East or in the Rhine Valley? (which either could align with some accounts.) EDIT: ... well, it could be both and I suppose I should add in Italy although I'm not sure why.

EDIT: I see VV was thinking the same (the "both" part.)

Both Ashkenazi U152 clusters have pretty logical European NPE origins:

U152+L2+L408+ "Epstein Cluster": This group traces its own history back to the middle Rhine area (Eppstein, Germany)

U152+Z56+L4 Cluster: There are 7 in this cluster, 6 are Ashkenazim and 1 is Catholic-Mexican with 0% Jewish ancestry as per Family Finder. I ran the TMRCA using Ken's Gen7 and the age came out to the end of the Roman period at 536 AD ± 338. L4's parent (Z56), seems to be have unusually high frequency in central Italy where it could make up about a third of all U152. So to me, a NPE during the Roman period is a no-brainer.

I don't think it is a coincidence that Ashkenazim with German last names are higher in U106 and U152 and those with Slavic last names are higher in R1a. That I know of, European SNPs are not very common in Sephardi Jews.
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Maliclavelli
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« Reply #38 on: August 01, 2012, 08:01:56 PM »

That I know of, European SNPs are not very common in Sephardi Jews.
But also amongst them happened many introgressions. I have studied the case of the Senior family, who has a haplotype close to mine (and my oldest ancestor was called “Signorino”). We have also paper trails that demonstrate that the Sephardic “Senyor” was a converted to Judaism who had many problems with the Community, after migrated to Holland and some of the descendants to the Isles. For what I have said before, the Sephardic R1b1* are probably introgressed from a Spaniard.

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« Reply #39 on: August 01, 2012, 09:39:36 PM »

Dienekes' latest age estimates table for the major haplogroups is not all that shocking.
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« Reply #40 on: August 01, 2012, 10:05:14 PM »

Dienekes' latest age estimates table for the major haplogroups is not all that shocking.

I can't resist commenting on the irony.

Hummm...for someone who swore off STR based calculations, he sure has no problem using Xue's mutation rate to calculate M343.

What a difference a year makes. Just scroll down to "UPDATE I (An epitaph for Y-STRs)." http://dienekes.blogspot.com/2011_08_01_archive.html  He summed it as
Quote from: Dienekes
The reason is simple: as clocks, they $/^#k.

Oh, well, I'm glad he decided not to throw the baby (STR diversity/generations) out with the bath water.


Am I reading the "N" column correctly? Some of the "N" values (counts) are 6, 8 and 1. If so, I wouldn't necessarily say he has a great data set to work with.

EDIT: I guess he's not using STRs in his estimates so my comment on irony was off. Please ignore.
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« Reply #41 on: August 01, 2012, 10:44:32 PM »

Oh, well, I'm glad he decided not to throw the baby (STR diversity/generations) out with the bath water.

Am I reading the "N" column correctly? Some of the "N" values (counts) are 6, 8 and 1. If so, I wouldn't necessarily say he has a great data set to work with.


Mike, not sure where you are getting at, but maybe you should know that Dienekes’s age estimates where done using SNPs, not STRs. He mentioned it earlier, that he is using the SNP mutation rate of 3*10-8 mutations/nucleotide/generation. Now, you are right to be skeptical of some of the haplogroups that have very small sample sizes.
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Richard Rocca
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« Reply #42 on: August 01, 2012, 10:54:17 PM »

Another BIG problem with SNP based TMRCA calculations is unknown SNPs. If we look at where M153 (aka Basque marker) was a year and a half ago (one level down from P312) to where we know it exists today (10 levels down from P312), we can see very quickly the issues that can present themselves.
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« Reply #43 on: August 02, 2012, 12:36:11 AM »

Oh, well, I'm glad he decided not to throw the baby (STR diversity/generations) out with the bath water.

Am I reading the "N" column correctly? Some of the "N" values (counts) are 6, 8 and 1. If so, I wouldn't necessarily say he has a great data set to work with.


Mike, not sure where you are getting at, but maybe you should know that Dienekes’s age estimates where done using SNPs, not STRs. He mentioned it earlier, that he is using the SNP mutation rate of 3*10-8 mutations/nucleotide/generation. Now, you are right to be skeptical of some of the haplogroups that have very small sample sizes.


I didn't realize he was counting SNP mutations. That's fair if he's sticking to his guns on NOT using STRs.

I have my concerns on counting SNPs. IF I remember correctly, VV tried this and felt there were a lot of bad reads in SNP test results.  Maybe the technology is better now.

I have another concern, at least in terms of youthful haplogroups.  Are SNPs very sporadic in their occurrence? If we don't have enough territory (Y chromosome) tested and enough good reads on SNP statuses I'm not sure if this is better than using only very slow STRs. The problem being that of using a calendar to measure hours.  We would need a huge sample of lineages, right?  Wouldn't it be a problem in that most ancient lineages went extinct so that cuts down on the data as far as number of different SNP branch lengths to survey? I guess that is why Dienekes is having to use a very limited sample size (column N) in some cases.

I don't know that much about this other than Karafet used it to get the R1 TMRCA of 18.5K ybp plus or minus a huge range.

Any comments on the reliability of SNPs for measuring time?
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« Reply #44 on: August 02, 2012, 01:45:24 AM »

"Some R1b chromosomes were likely in Jewish populations per-diaspora while others were likely introduced post-diaspora."

There can only be one Cohen line with descent from Aaron if he actually existed and strict adherence to a priestly caste was maintained. Either it is R1b or IJ. It cannot be both.

"Y-chromosomal Aaron is the name given to the hypothesised ancestor of the Kohanim, a patrilineal "priestly caste " in Judaism. In Scripture, this ancestor is identified as Aaron, the brother of Moses. This has come about since the appearance in the 1990s of some relevant publications, relevant to the patrilineal ancestor of all humans, Y-chromosomal Adam."

Levant is also home to people of non Semitic descent.

As for example, Galil goyim Isaiah 9:1

The region takes its name from the Hebrew galil, "district", "circle", a noun which, in the construct state, requires a genitival noun. Hence the Biblical "Galilee of the Nations", Hebrew"galil goyim"(Isaiah 9:1). The "nations" would have been the foreigners who came to settle there, or who had been forcibly deported there. The


  Indo-European Phillistines,


In Genesis 21, Abraham agreed a covenant of kindness with the Philistine king Avimelech and his descendants.

It is not hard to entertain the idea that there was mixing between the communities, as can be seen in more recent times, and reported in the study

 Phylogeographic analysis of paternal lineages in NE Portuguese Jewish communities



"A deeper and more detailed investigation is required to clarify how these communities avoided the expected inbreeding caused by over four centuries of religious repression. Concerning haplogroup lineages, we detected some admixture with the Western European non-Jewish populations (R1b1b2-M269, ∼28%), along with a strong ancestral component reflecting their origin in the Middle East [J1(xJ1a-M267), ∼12%; J2-M172, ∼25%; T-M70, ∼16%] and in consequence Trás-os-Montes Jews were found to be more closely related with other Jewish groups, rather than with the Portuguese non-Jewish population. Am J Phys Anthropol 2010. © 2009 Wiley-Liss, Inc"

    Inês Nogueiro1,
    Licínio Manco1,
    Verónica Gomes2,3,
    António Amorim2,4,
    Leonor Gusmão2,*
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« Reply #45 on: August 02, 2012, 02:32:15 AM »

Any comments on the reliability of SNPs for measuring time?

I think Richard Rocca's post sums it up well.


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« Reply #46 on: August 02, 2012, 04:14:06 AM »

Another BIG problem with SNP based TMRCA calculations is unknown SNPs. If we look at where M153 (aka Basque marker) was a year and a half ago (one level down from P312) to where we know it exists today (10 levels down from P312), we can see very quickly the issues that can present themselves.
This objection is a real but does not apply to the method Dienekes is using. 

His method depends on completely re-sequencing large chunks of the Y chromosome (and, importantly, the SAME chunks for each sample).  The distance between the samples - as computed for just those chunks - is then calculated and scaled by the mutation rate.  In effect, as far as his estimates go, there are theoretically no  "unknown SNPs".

I do have a concern about the R-M269 estimates because it is quite likely that the 1000 Genomes project specifically chose to sequence regions of the Y known to be polymorphic based on prior testing and that prior testing always includes R-M269 research samples.  This is one reason I don't trust the estimate for R1b1a2a1a1a5:  it likely includes more SNPs peculiar to this clade than you would expect if you chose the sequencing region completely at random.  So the TMRCA that Dienekes estimates for R1b1a2a1a1a5 is probably too old by a significant margin.

This effect moderates pretty quickly as you move upstream, though, so ascertainment bias probably does not impact the majority of his time estimates significantly including the R-L389 estimate.

VV
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« Reply #47 on: August 02, 2012, 04:49:05 AM »

I do have a concern about the R-M269 estimates because it is quite likely that the 1000 Genomes project specifically chose to sequence regions of the Y known to be polymorphic based on prior testing and that prior testing always includes R-M269 research samples.  This is one reason I don't trust the estimate for R1b1a2a1a1a5:  it likely includes more SNPs peculiar to this clade than you would expect if you chose the sequencing region completely at random.  So the TMRCA that Dienekes estimates for R1b1a2a1a1a5 is probably too old by a significant margin.

Then the 1KGP would be U106 biased! But then why out of 51 Tuscans we have had 15 U152 and 15 J?
And  2 R-L51, almost 4%, which is the percentage in line with Central North Italy? (I am going by heart, but these should be the percentages).
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« Reply #48 on: August 02, 2012, 04:53:43 AM »

In case we should ask Dienekes who are these 109 people, because I ask me where are the Indian (Gujaratis) R-M207-s?
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« Reply #49 on: August 02, 2012, 07:24:16 AM »

@Stan
Would you mind explaining how you arrived to the conclusion that one SNP event can be estimated as occurring every 628 years?

I gotta admit, I'm rather confused by the methodology that Dienekes is using. I know Karafet.et.al.2008 did an interpolation methodology, where  the age of CT was fixed at 70 kya, and based on how downstream each SNP was with respect to CT, the age was calculated.

What I know is that the paternal germ-line autosomal mutation rates are much faster than maternal germ-line rates. Also, the mutation rate used by Dienekes was 3*10-8 mutations/nucleotide/generation. The y-chromosome has about 56 millions nucleotides, of course, I'm not sure how big the NRY section is, in terms of nucleotides, but most of the Y-chromosome is non-recombinant. So like I said before, I would greatly appreciate it, if you could explain how you came to the 628 years/SNP conclusion.

The SNP mutation rate in the human genome, according to textbooks of genetics, amounts to 3x10^-8 SNP per 1 base pair per the generation (30 years), that is 1x10^-9 SNP/ 1 bp/ 1 year, that is 0.000,000,001 SNP/1 bp/1 year.

But this rate of the mutation were calibrated for the time of 5,000,000 years from the moment of the divergence of the man and the chimpanzee. Now it is known, that it is necessary to calibrate this rate for 6,000,000 years; so is necessary to multiply it through 5/6. The rezult: 0.000,000,00083333 SNP

Moreover it is known, that SNP mutations in Y-chromosome are occurring 4.8 times more quickly than in the entire human genome (geneticists are trying to somehow explain this phenomenon with environmental conditions of meiosis: http://en.wikipedia.org/wiki/Y_chromosome). The above rate it is necessary so to multiply through 4.8.
In the result we receive 0.000,000,004 SNP/1 base pair/1 year in NRY
................................
In most precisely tested haplogroup (e.g. R1b) we are finding
average about 164 SNPs per about 400,000 base pair in WTY (in ISOGG and TreeDraft by T. Krahn).
It is equaling 0.00041 SNPs per 1 base pair

Dividing this result by 0.000,000,004 SNP per year (in NRY) ,
we receive the result 102,500 ybp, i.e. about 103,000 ybp.
It means 1 SNP per 628 years.
Stan

Supplement
In C-T: average 115 SNPs; x 628 = 72,000 years
In R1b: average 30 SNPs, x 628 = 18,800 years
In R1a: average 25 SNPs, x 628 = 15,700 years
« Last Edit: August 02, 2012, 07:46:20 AM by Elkate » Logged

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