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Author Topic: Atlantic Modal Haplotype  (Read 1131 times)
Jarman
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« on: July 01, 2012, 06:15:29 PM »

The modals for P312 and U106 both closely resemble the Atlantic Modal Haplotype. So my question is where was the first AMH born? I suppose I've asked for the impossible, but couldn't this be the origin of L11?
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Humanist
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« Reply #1 on: July 01, 2012, 07:20:57 PM »

I do not have an answer to your question, but here are three haplotypes that may be of some relevance:

Code:
POP 393 390 19 391 385 385 426 388 439 389i 392 389ii
LIC 13 23 14 11 11 14 xx xx 12 13 13 29
DRZ 13 24 14 11 xx xx 12 12 ?? 13 13 29
ALW  13     24    14     11    11    15     xx     xx    xx     13    13    29

LIC = Lichtenstein Cave Data Analysis 2008-03-23

Quote:
Quote
The skeletons of 21 females and 19 males were identified in the cave. The items...found in the cave are typical for the regional time period of 1000 to 700 B.C.E....

DRZ = Druze modal
ALW = Alawite second most frequent R1b haplotype
« Last Edit: July 01, 2012, 07:28:17 PM by Humanist » Logged

Mike Walsh
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« Reply #2 on: July 04, 2012, 02:32:11 AM »

The modals for P312 and U106 both closely resemble the Atlantic Modal Haplotype. So my question is where was the first AMH born? I suppose I've asked for the impossible, but couldn't this be the origin of L11?

What data are you looking at?  I get that P312's modal is the Atlantic Modal haplotype.

My guess is that the Most Recent Common Ancestor of P312 folks has this haplotype. It is quite possible that the L11* Most Recent Common Ancestor for P312 and U106 was the same haplotype.
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JeanL
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« Reply #3 on: July 04, 2012, 12:51:04 PM »

My guess is that the Most Recent Common Ancestor of P312 folks has this haplotype. It is quite possible that the L11* Most Recent Common Ancestor for P312 and U106 was the same haplotype.

That guess assumes that the MRCA of all P312 folks lived within the time frame of the time of fixation of even the fast mutating STRs in your 111, 67, 37, 25 or 12 STRs markers series. As for L11+ having the same haplotype, not really, simply the most common haplotype today is that of P312’s MRCA, therefore under the assumption of least amount of mutations the P312 modal gets picked as the L11+ modal. However, I’ve come to realize that under a Wright-Fisher expanding model, the assumption of least amount of mutations, or most common haplotype describing the “phantom”/”ancestral”/”modal” has the implicit assumption that the MRCA of the set lived within the timeframe of the time of fixation of your fast mutating STRs, otherwise your TMRCA might be underestimated by a factor of 2 or more.
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Jarman
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« Reply #4 on: July 04, 2012, 04:11:49 PM »

That guess assumes that the MRCA of all P312 folks lived within the time frame of the time of fixation of even the fast mutating STRs in your 111, 67, 37, 25 or 12 STRs markers series. As for L11+ having the same haplotype, not really, simply the most common haplotype today is that of P312’s MRCA, therefore under the assumption of least amount of mutations the P312 modal gets picked as the L11+ modal. However, I’ve come to realize that under a Wright-Fisher expanding model, the assumption of least amount of mutations, or most common haplotype describing the “phantom”/”ancestral”/”modal” has the implicit assumption that the MRCA of the set lived within the timeframe of the time of fixation of your fast mutating STRs, otherwise your TMRCA might be underestimated by a factor of 2 or more.

Can you please further explain "time of fixation" and put a date to it?  Also we are not just looking at the P312 modal - the U106 modal is almost a twin, and among those who have examined the U106 modal is a sentiment that without the L48 family the DYS390 modal is 24. So I believe we are looking at L11 as likely matching the AMH because it is the parent of two haplogroups with markers matching the AMH.
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JeanL
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« Reply #5 on: July 04, 2012, 05:55:08 PM »

Can you please further explain "time of fixation" and put a date to it?

I can give it a try, the time of fixation is the amount of time it takes under a Wright-Fisher model for a mutation to become fixated in a population, that is reach a frequency of 1. Generally speaking, this applies to SNP mutations, and is a function of the effective population size and mutation rate. Now, in the case of STRs, a mutation usually gets fixed in N number of generations, now fixed in this case doesn’t mean that it reaches frequency of 1, but that it becomes the majority mutation. Now the way to calculate N in case of STRs is N can be estimated as 1/μ, where μ is the mutation rate. For example any STR “A” with a mutation rate of say 0.001 would become fixated (reach majority frequency) in a population in 1000 generations. That means that if there was an expanding population which hasn’t undergone a bottleneck, an ancestral value of x would reach majority frequencies an become x+1 in 1000 generations. So when one samples a random subset of individuals from that population gets sampled say 1500 generations into the future, the vast majority of haplotypes would have x+1 allele value in that given locus, so it would seem as if the modal/ancestral value was x+1, and it would seem fairly logical, because there would still be a minority element of x, x+2, x-1, allele values, leading someone into the notion that the TMRCA of that population is that measured using the distance between the amount of mutations off the modal value x+1. But in reality the ancestral value was not x+1 but x, but the notion that the modal value is such value that minimizes the amount of mutation in a population would indeed lead any model out there to pick x+1 as the modal value. Hence why I said, that the is an intrinsic assumption that the TMRCA of any population is more recent than the time of fixation of the fast mutating STRs, and hence why I argued before that using a mixed set of STRs undermines the TMRCA.

Also we are not just looking at the P312 modal - the U106 modal is almost a twin, and among those who have examined the U106 modal is a sentiment that without the L48 family the DYS390 modal is 24. So I believe we are looking at L11 as likely matching the AMH because it is the parent of two haplogroups with markers matching the AMH.

In order for L11 ancestral allele values to match the AMH, it means that the time when either the P312 or U106 mutations occurred has to be less than the time of fixation for any given locus. Is the modal of all L11+ today possibly the AMH? Could be. Was the ancestral haplotype of the L11 man who gave rise to P312, and the L11 man who gave rise to U106 the AMH? Depends on the time frame, if is recent, then yes for STR that has a mutation rate that yields a time of fixation older than that. 
« Last Edit: July 04, 2012, 05:58:29 PM by JeanL » Logged
Mike Walsh
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« Reply #6 on: July 05, 2012, 12:19:50 AM »

My guess is that the Most Recent Common Ancestor of P312 folks has this haplotype. It is quite possible that the L11* Most Recent Common Ancestor for P312 and U106 was the same haplotype.

That guess assumes that the MRCA of all P312 folks lived within the time frame of the time of fixation of even the fast mutating STRs in your 111, 67, 37, 25 or 12 STRs markers series. As for L11+ having the same haplotype, not really, simply the most common haplotype today is that of P312’s MRCA, therefore under the assumption of least amount of mutations the P312 modal gets picked as the L11+ modal. However, I’ve come to realize that under a Wright-Fisher expanding model, the assumption of least amount of mutations, or most common haplotype describing the “phantom”/”ancestral”/”modal” has the implicit assumption that the MRCA of the set lived within the timeframe of the time of fixation of your fast mutating STRs, otherwise your TMRCA might be underestimated by a factor of 2 or more.
I agree that the general L11 modal is going to be dominated by P312, since it is he largest group of haploypes we have.

However, the modal for L11* (L11+ P312+ U106-) is only four off P312's at 111 STRs and I don't think any of these are slow markers.  P312's modal might be the true ancestral haplotype for the L11 Most Recent Common Ancestor, or maybe it is L11*'s modal that is the true ancestral.  Either way there is very little difference between the two.
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Jarman
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« Reply #7 on: July 05, 2012, 05:20:53 PM »

I agree that the general L11 modal is going to be dominated by P312, since it is he largest group of haploypes we have.
However, the modal for L11* (L11+ P312+ U106-) is only four off P312's at 111 STRs and I don't think any of these are slow markers.  P312's modal might be the true ancestral haplotype for the L11 Most Recent Common Ancestor, or maybe it is L11*'s modal that is the true ancestral.  Either way there is very little difference between the two.

I believe an important point can be made here regarding L11's modal similarity to the AMH as well as to the P312 and U106 modals.  Several places I have read the thinking that because of their similarities, the origins of both P312 and U106 had to be in close proximity. But that is not neccessarilly so if L11's modal is close or equal the AMH - the geographic origins of P312 and U106 could be as far apart as L11's geographic distribution at the time of Mr. P312's and Mr. U106's birth. Increasing our knowledge re P312 and U106 requires learning much much more about L11.
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Mike Walsh
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« Reply #8 on: July 05, 2012, 08:13:32 PM »

I agree that the general L11 modal is going to be dominated by P312, since it is he largest group of haploypes we have.
However, the modal for L11* (L11+ P312+ U106-) is only four off P312's at 111 STRs and I don't think any of these are slow markers.  P312's modal might be the true ancestral haplotype for the L11 Most Recent Common Ancestor, or maybe it is L11*'s modal that is the true ancestral.  Either way there is very little difference between the two.

I believe an important point can be made here regarding L11's modal similarity to the AMH as well as to the P312 and U106 modals.  Several places I have read the thinking that because of their similarities, the origins of both P312 and U106 had to be in close proximity. But that is not neccessarilly so if L11's modal is close or equal the AMH - the geographic origins of P312 and U106 could be as far apart as L11's geographic distribution at the time of Mr. P312's and Mr. U106's birth. Increasing our knowledge re P312 and U106 requires learning much much more about L11.
.. and L51 too.  Whether L51 is just a little older than L11 or a lot makes a difference.  Unfortunately L51* is a little hard too find, at least relative to P312 and U106.

As far as that goes, L11* not very plentiful and is quite scattered - today.
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Jarman
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« Reply #9 on: July 09, 2012, 04:47:55 PM »

In the absense of SNP data, are there any Y haplotypes for Beaker Folk (other than Lichtenstein Cave)? Any western Beaker Y haplotypes?
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rms2
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« Reply #10 on: July 10, 2012, 06:24:33 AM »

The Lichtenstein Cave is not a Beaker site. It is much too late, and it is just not Beaker. Lee et al recovered R-M269 (xU106) and R-M343 (xU106) from remains at a Beaker site near Kromsdorf, Germany, but they didn't publish any haplotypes.
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