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Author Topic: The "randomness" of the STR Mutational process  (Read 2460 times)
Jean M
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« Reply #25 on: June 11, 2012, 09:11:19 AM »

I have that book as a reference.  for what we are discussing here, it is out of date.

A second edition is in progress, but that does not affect the basic fact that dating estimates from mutation rates have to be externally calibrated. That is part of the ABC of the subject, you might say. Best not to lose sight of it in a mass of numbers. No amount of number-crunching can produce internal validation for its own results.
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ironroad41
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« Reply #26 on: June 11, 2012, 10:28:57 AM »

I believe it is a little more complicated than that.  When I approached the Ian Cam, my external data was the name, Gregor of the Golden Bridles and approximate birthdate.  I then had to "learn" the data set and identify those entries that were closely related such that they both possessed the same mutation and eliminate the redundancy.  The best set of data I found was a set of some 20 to 30 persons, all with different mutations clustered around the middle mutation rate dys loci.  I couldn't use the faster mutators since the probability of more than one mutation or a hidden mutation was too high.  I excluded an entry with a 426 mutation since I didn't have a large enough data set.  It was intelligent cherry picking, in which certain properties of the dys loci were known.

The major point I am making here is that without a lot of detailed knowledge about the data set, you can't make an intelligent estimate of the TMRCA, which is presumably unknown.  In my judgment the bottleneck is a big issue.  It at least separates the data into two piles?  Furthermore the younger data set is usually the largest and drives the modal values and the TMRCA.  Even with Klyosovs method we are left with many of the same questions: e.g. do we have the right modal, are the entries independent, etc.

So an external data point, such as the founding date of the Maori invasion of New Zealand may provide guidance, but without some good understanding of the properties of the mutational process, we can still go astray.
« Last Edit: June 11, 2012, 10:30:02 AM by ironroad41 » Logged
Mike Walsh
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« Reply #27 on: June 11, 2012, 10:53:25 AM »

.... Can we create a new estimate of Hg age using this assumption.  For instance, I showed (having 8 mutations) that my haplotype is separated from M269/P25 by 40 K years.  Does that make any sense? ....

You use the word "show" and I equate that to "demonstrate."  These are fairly assertive term indicating you have provided some level of proof of what you are saying.  I missed that evidence and logic or I guess I maybe just misunderstood it or forgot it.

How have you shown that your haplotype is separated from M269 or P25 by 40K years and which is it? M269 or P25?
 If you accept Klyosovs assertions of his approach, then I have demonstrated that fact.

I used the set of 22 dys loci values klyosov calls R1b1.  This is in his Out of AFrica paper published on-line May 2012.

Does anyone here accept Klyosov's assertions, carte blanche?  I certainly don't, and as you know some of the stronger statistically oriented hobbyists don't either.

Are you applying Klyosov's assertions properly? Would he say you can use average mutation rates to a single instance and get a precise result?

So which was it? 40K years from M269 or P25.   Is this your way of answering that Klyosov has a haplotype he calls R1b1.  ISOGG lists P25 as a defining SNP for R1b1 so are you saying P25?    Does that mean we should forget that you also said M269 and you really didn't mean M269?
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Jean M
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« Reply #28 on: June 11, 2012, 11:04:23 AM »

When I approached the Ian Cam, my external data was the name, Gregor of the Golden Bridles and approximate birth date.

But did you understand that not all the people today with the surname McGregor will be descended from Gregor of the Golden Bridles? Did you restrict the data-set to those clearly related to the Ian Cam? In other words did you exclude yourself and others who are of a different haplogroup? If you didn't then you are unlikely to get an estimate in line with the approximate birth date of Gregor of the Golden Bridles.

As far as I can tell, you are unrelated to the Ian Cam. So the lineage of the Ian Cam will tell you absolutely nothing about your own ancestry.  It seems a shame that you wasted so much time on it. But that's how things often go in genealogy. People pursue all sorts of false leads.
« Last Edit: June 11, 2012, 11:08:30 AM by Jean M » Logged
ironroad41
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« Reply #29 on: June 11, 2012, 11:11:34 AM »

The keeper of the Clan Gregor web site is Dr. Richard McGregor, who by the way is also Z 253 like I am.  For purposes of the studies I've performed I only use the Ian Cam entries, who are all believed to be descendants of the Ian Cam.

The first test of this claim is a 10 at 391, which is characteristic of the Ian Cam members.  That said, family history plays a role in being included in that data set.

BTW: thats a pretty trivial question for you to ask.  I've explained this all before and I thought you understood that point.
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Mike Walsh
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« Reply #30 on: June 11, 2012, 11:19:48 AM »

The keeper of the Clan Gregor web site is Dr. Richard McGregor, who by the way is also Z 253 like I am.  For purposes of the studies I've performed I only use the Ian Cam entries, who are all believed to be descendants of the Ian Cam.

The first test of this claim is a 10 at 391, which is characteristic of the Ian Cam members.  That said, family history plays a role in being included in that data set. ...

Are you talking about this subgrouping - "MacGregor (Ian Cam)" ?
http://www.familytreedna.com/public/macgregor/default.aspx?section=yresults

I see it has a lot of 391=10.  Didn't MaJost run TMRCA estimate on this?  What came up?
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ironroad41
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« Reply #31 on: June 11, 2012, 11:20:55 AM »

.... Can we create a new estimate of Hg age using this assumption.  For instance, I showed (having 8 mutations) that my haplotype is separated from M269/P25 by 40 K years.  Does that make any sense? ....

You use the word "show" and I equate that to "demonstrate."  These are fairly assertive term indicating you have provided some level of proof of what you are saying.  I missed that evidence and logic or I guess I maybe just misunderstood it or forgot it.

How have you shown that your haplotype is separated from M269 or P25 by 40K years and which is it? M269 or P25?
 If you accept Klyosovs assertions of his approach, then I have demonstrated that fact.

I used the set of 22 dys loci values klyosov calls R1b1.  This is in his Out of AFrica paper published on-line May 2012.

Does anyone here accept Klyosov's assertions, carte blanche?  I certainly don't, and as you know some of the stronger statistically oriented hobbyists don't either.

Are you applying Klyosov's assertions properly? Would he say you can use average mutation rates to a single instance and get a precise result?

So which was it? 40K years from M269 or P25.   Is this your way of answering that Klyosov has a haplotype he calls R1b1.  ISOGG lists P25 as a defining SNP for R1b1 so are you saying P25?    Does that mean we should forget that you also said M269 and you really didn't mean M269?
 Whether I or anyone else accepts Klyosovs assertions he is a peer reviewed publisher ( whatever thats worth?).  I'm not sure he accepts the variance approach either for what its worth.

Its his approach.  he uses an average number for any of the 22 slowest mutators.  I just plugged it in and voila.

I don't want to get into a big discussion of whats what in the ISOGG list.  He called the SNP  R1b1 in his paper.   I didn't say M269, I just said it as I saw it as being one or other, he didn't specify and apparently he's rewriting early history.  According to the list I have it is P25, but it may be out of date.
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ironroad41
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« Reply #32 on: June 11, 2012, 11:27:49 AM »

The keeper of the Clan Gregor web site is Dr. Richard McGregor, who by the way is also Z 253 like I am.  For purposes of the studies I've performed I only use the Ian Cam entries, who are all believed to be descendants of the Ian Cam.

The first test of this claim is a 10 at 391, which is characteristic of the Ian Cam members.  That said, family history plays a role in being included in that data set. ...




Are you talking about this subgrouping - "MacGregor (Ian Cam)" ?
http://www.familytreedna.com/public/macgregor/default.aspx?section=yresults

I see it has a lot of 391=10.  Didn't MaJost run TMRCA estimate on this?  What came up?
Yes, he did and I believe his best estimate using 5 111 dys loci entries was essentially about 1350 AD.

The Clan Gregor is a large data set.  It has Greggs, Griers, Gregorys and a lot of miscellaneous entries.  The 391 = 10 is the defining mutation for the Ian Cam as I said.  That said, it posseses all the little snarls that make TMRCA estimates tough as I've outllned before.

Until the present chief got 68 to 111 dys loci measured, he had shown no mutations from the modal.  He now has three, which argues that 111 dys loci are probably necessary for most estimates?
« Last Edit: June 11, 2012, 11:30:35 AM by ironroad41 » Logged
Jean M
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« Reply #33 on: June 11, 2012, 11:31:00 AM »

The keeper of the Clan Gregor web site is Dr. Richard McGregor, who by the way is also Z 253 like I am.  

I'm not disputing your right to consider yourself part of Clan Gregor. You are certainly not on your own in that desire. I'm just concerned that readers here understand what you are talking about. Essentially there are two data-sets within the MacGregor project, the Ian Cam and the rest. Only the former can or should be related to the date for Ian Cam/Gregor of the Golden Bridles.

Lumping together the other, unrelated lineages is liable to give you a far older date, that is unrelated to any surname. These people may like to consider themselves part of a clan, but they in fact are probably a mixture of unrelated men who adopted the surname to attach themselves to the chief's line, or people who just happen to descend from another Gregor.
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Jean M
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« Reply #34 on: June 11, 2012, 11:36:35 AM »

Yes, he did and I believe his best estimate using 5 111 dys loci entries was essentially about 1350 AD.

Good enough. "most historians agree that the first certain Chief was Gregor "of the Golden Bridles." Gregor's son, Iain Camm ("of the One-Eye") succeeded as the second Chief sometime prior to 1390." (Wikipedia).
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Mike Walsh
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« Reply #35 on: June 11, 2012, 12:13:54 PM »

The keeper of the Clan Gregor web site is Dr. Richard McGregor, who by the way is also Z 253 like I am. For purposes of the studies I've performed I only use the Ian Cam entries, who are all believed to be descendants of the Ian Cam.

The first test of this claim is a 10 at 391, which is characteristic of the Ian Cam members.  That said, family history plays a role in being included in that data set. ...

Are you talking about this subgrouping - "MacGregor (Ian Cam)" ?
http://www.familytreedna.com/public/macgregor/default.aspx?section=yresults

I see it has a lot of 391=10.  Didn't MaJost run TMRCA estimate on this?  What came up?
Yes, he did and I believe his best estimate using 5 111 dys loci entries was essentially about 1350 AD.

The Clan Gregor is a large data set.  It has Greggs, Griers, Gregorys and a lot of miscellaneous entries.  The 391 = 10 is the defining mutation for the Ian Cam as I said.  That said, it posseses all the little snarls that make TMRCA estimates tough as I've outllned before.

Until the present chief got 68 to 111 dys loci measured, he had shown no mutations from the modal.  He now has three, which argues that 111 dys loci are probably necessary for most estimates?

I'm not disputing your right to consider yourself part of Clan Gregor. You are certainly not on your own in that desire. I'm just concerned that readers here understand what you are talking about. Essentially there are two data-sets within the MacGregor project, the Ian Cam and the rest. Only the former can or should be related to the date for Ian Cam/Gregor of the Golden Bridles.

Lumping together the other, unrelated lineages is liable to give you a far older date, that is unrelated to any surname. These people may like to consider themselves part of a clan, but they in fact are probably a mixture of unrelated men who adopted the surname to attach themselves to the chief's line, or people who just happen to descend from another Gregor.

I think Jean M has a good point.  For clarity sake, the project admins on the Clan Gregor project should consider breaking apart the "MacGregor (Ian Cam)" subgrouping to separate subgroups.

That subgroup has 102 haplotypes.  79 of those 102 match are matches with the Scots Modal, or what I call variety 1030-A-Sc. They typically are typically 391<=10 449>=30 444>=11 413a<=22  531>=12 GataH4=12 and either YCAII=19,24 or YCAII=19,22. Your STRs are NOT like those 79.

Separately, I can find at least 10 clear 1030-A-Sc people who have tested for Z253. They are all Z253-. They are 16273 Anderson, f10348 Lee, f57711 McDonald, f153130 Moore, fN36830 Moore, f108937 Neilson, f66126 Taylor, f120820 MacFarland, f147012 Young, f143812 MacRae.

Mutations to 391=10 for the 102 people in "MacGregor (Ian Cam)" are a probably result of convergence, at least two separate events that happened in separate lineages.

This is the beauty of SNPs. They are truth tellers. Since Dr. Richard McGregor and yourself are Z253+, you can not possibly be closely related to the 1030-A Sc (Scots) people who are Z253-.   As Z253+ folks, you are more closely related to Irish III (L226+) and Irish IV/Continental folks and even a couple of Iberian descent folks than you are to 1030-A-Sc (Scots) folks.

I have no comment on what lineages are true "MacGregor (Ian Cam)" or not. I have no idea. I am just saying that the "MacGregor (Ian Cam)" has at least two lineages that are not related any closer than 2000-3000 years ago.  If you believe in the Zhiv evolutionary rates you might want to triple or quadruple that.
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« Reply #36 on: June 11, 2012, 12:17:17 PM »

The keeper of the Clan Gregor web site is Dr. Richard McGregor, who by the way is also Z 253 like I am.  

I'm not disputing your right to consider yourself part of Clan Gregor. You are certainly not on your own in that desire. I'm just concerned that readers here understand what you are talking about. Essentially there are two data-sets within the MacGregor project, the Ian Cam and the rest. Only the former can or should be related to the date for Ian Cam/Gregor of the Golden Bridles.

Lumping together the other, unrelated lineages is liable to give you a far older date, that is unrelated to any surname. These people may like to consider themselves part of a clan, but they in fact are probably a mixture of unrelated men who adopted the surname to attach themselves to the chief's line, or people who just happen to descend from another Gregor.

There is another consideration as well, which may or may not have been taken into account.

The Ian Cam group is united because they are Scots Modal, at a rough guess from looking through the L21 project the other day I'd say Scots Modal could make up to 5% of the kits there.

MacGregor and its variations are quite common and just because you are Scots Modal and carry a MacGregor variant surname doesn’t necessarily mean you descend from Iain Camm.
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« Reply #37 on: June 11, 2012, 12:20:32 PM »

Are you applying Klyosov's assertions properly? Would he say you can use average mutation rates to a single instance and get a precise result?
 

Mike, he does use mutation constants per haplotypes, which I think is complete bull, given the ratio observed between the standard deviation and the mean mutation rate per haplotype.

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ironroad41
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« Reply #38 on: June 11, 2012, 12:20:55 PM »

The keeper of the Clan Gregor web site is Dr. Richard McGregor, who by the way is also Z 253 like I am.  

I'm not disputing your right to consider yourself part of Clan Gregor. You are certainly not on your own in that desire. I'm just concerned that readers here understand what you are talking about. Essentially there are two data-sets within the MacGregor project, the Ian Cam and the rest. Only the former can or should be related to the date for Ian Cam/Gregor of the Golden Bridles.

Lumping together the other, unrelated lineages is liable to give you a far older date, that is unrelated to any surname. These people may like to consider themselves part of a clan, but they in fact are probably a mixture of unrelated men who adopted the surname to attach themselves to the chief's line, or people who just happen to descend from another Gregor.
Your first statement is correct.  But there are many subsets as I've noted. The Greggs, Griers, Gregorys etc.  The name MacGregor was outlawed by the British for most of 17th and 18th century.  

I have run TMRCA's on many of the subsets and do get numbers usually within the range of  500 BC (Richard McGregor and I and others) to early AD for other groups.  Most of us are Partakers, although, there is some disagreement as to the original source of the name "Gregor", Giric, Gregory?
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« Reply #39 on: June 11, 2012, 12:35:03 PM »

Whether I or anyone else accepts Klyosovs assertions he is a peer reviewed publisher ( whatever thats worth?).  I'm not sure he accepts the variance approach either for what its worth.

 

Ironroad if you look here:

http://aklyosov.home.comcast.net/~aklyosov/

You will see that most of Klyosov’s publications have been made in the:

“Proceedings of the Russian Academy of DNA Genealogy”

Which I’m pretty sure is his own Journal, then he has published Journal of Genetic Genealogy, a Journal called Biochemistry(Moscow), and in Advances in Anthropology. Don’t be fooled by his claims that he published in Human Genetics or Nature, he hasn’t, he published a comment regarding a study that was published in Human Genetics, and he has submitted two papers to Nature Proceedings, but they never made it to any of Nature Journals. He claims that it is because they requested him to shorten the length of the article, and he didn’t feel like it. As for Advances in Anthropology, it is a fairly recent Journal, and from the looks of it is not hard to get published in it, very likely the peer-reviewing process isn’t done, or it doesn’t go into the details, the same goes for Journal of Genetic Genealogy, they are more of hobbyist journals. Actually Advances in Anthropology might get some points, because Lacan et.al team published this paper over  there:

A Time Series of Prehistoric Mitochondrial DNA Reveals Western European Genetic Diversity Was Largely Established by the Bronze Age

But that paper was more of a review than anything else. Klyosov has probably scored some good points publishing in that Journal, because it seems promising, but it doesn’t change the fact, that he is hardly what one would call a “peer reviewed” publisher.
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« Reply #40 on: June 11, 2012, 12:41:49 PM »

Are you applying Klyosov's assertions properly? Would he say you can use average mutation rates to a single instance and get a precise result?
 

Mike, he does use mutation constants per haplotypes, which I think is complete bull, given the ratio observed between the standard deviation and the mean mutation rate per haplotype.

What is "bull" is a TBD at this point.  In his paper published in May he asserts that the mutation rate constant for the 22 marker haplotypes equals to .0060 mutations/haplotype/conditional generation of 25 years .  8 mutations between R1b1 and myself results in 8/.006 = 1333 generations. The fudge factor for back mutations is 1.22 X 1333 = 1626 X 25 = 40,600 years.  This is an estimate of the time between R1b1 and my haplotype.

I do not say that this is all correct.  But I would argue that the use of the slowest mutators makes sense and corrrecting for back mutations makes sense.  It puts the GD argument in perspective, all mutations are not equal.  Apparently Klyosov has published a paper re: the derivation of .006.


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« Reply #41 on: June 11, 2012, 12:52:52 PM »

Are you applying Klyosov's assertions properly? Would he say you can use average mutation rates to a single instance and get a precise result?
 

Mike, he does use mutation constants per haplotypes, which I think is complete bull, given the ratio observed between the standard deviation and the mean mutation rate per haplotype.


What is "bull" is a TBD at this point.  In his paper published in May he asserts that the mutation rate constant for the 22 marker haplotypes equals to .0060 mutations/haplotype/conditional generation of 25 years .  8 mutations between R1b1 and myself results in 8/.006 = 1333 generations. The fudge factor for back mutations is 1.22 X 1333 = 1626 X 25 = 40,600 years.  This is an estimate of the time between R1b1 and my haplotype.

I do not say that this is all correct.  But I would argue that the use of the slowest mutators makes sense and corrrecting for back mutations makes sense.  It puts the GD argument in perspective, all mutations are not equal.  Apparently Klyosov has published a paper re: the derivation of .006.


I've a feeling even Klyosov would tell you there's something wrong with your methodology here.
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« Reply #42 on: June 11, 2012, 01:34:01 PM »

Whether I or anyone else accepts Klyosovs assertions he is a peer reviewed publisher ( whatever thats worth?).  I'm not sure he accepts the variance approach either for what its worth.

 

Ironroad if you look here:

http://aklyosov.home.comcast.net/~aklyosov/

You will see that most of Klyosov’s publications have been made in the:

“Proceedings of the Russian Academy of DNA Genealogy”

Which I’m pretty sure is his own Journal, then he has published Journal of Genetic Genealogy, a Journal called Biochemistry(Moscow), and in Advances in Anthropology. Don’t be fooled by his claims that he published in Human Genetics or Nature, he hasn’t, he published a comment regarding a study that was published in Human Genetics, and he has submitted two papers to Nature Proceedings, but they never made it to any of Nature Journals. He claims that it is because they requested him to shorten the length of the article, and he didn’t feel like it. As for Advances in Anthropology, it is a fairly recent Journal, and from the looks of it is not hard to get published in it, very likely the peer-reviewing process isn’t done, or it doesn’t go into the details, the same goes for Journal of Genetic Genealogy, they are more of hobbyist journals. Actually Advances in Anthropology might get some points, because Lacan et.al team published this paper over  there:

A Time Series of Prehistoric Mitochondrial DNA Reveals Western European Genetic Diversity Was Largely Established by the Bronze Age

But that paper was more of a review than anything else. Klyosov has probably scored some good points publishing in that Journal, because it seems promising, but it doesn’t change the fact, that he is hardly what one would call a “peer reviewed” publisher.

I could essentially post the same type of post re: variance as developed by Nordtvedt.  Its origin is in earlier papers by Goldstein and Stumpf, Science, 2001, march issue.

I am not supporting Klyosov, I am simply evaluating/ showing what his technique for estimating longer periods of time results in.

There have been extensive discussions on the variance approach on other boards, it has been supported by some vocal advocates, but never proven.  From what I've seen about Klyosov is that, to date, he hasn't been beaten down and he finally has some supporters?

For myself I have worked with Dr. Richard McGregor and Dr. Neil MacGregor on the MacGregor data set for almost five years.  We don't fully agree on everything but I think we have a common agreement on the Ian Cam and who the membership is.  Note: Richard is a musician and Neil is a biochemist.

I have spent most of my studies trying to understand the nature of STR's. It is part of my understanding gleaned from studying the Ian Cam.  From these studies I have developed a distrust of just throwing a set of entries together and using some basic equations to develop coalescent ages or whatever.  Some folks are more in love with developing an elegant theory, not understanding the data.

Richard publishes some good annual reviews about the status of clan gregor available at the Clan Gregor web site.

There is a Japanese Koan that goes: Are Enlighted people subject to causality.  The answer is :  They are not blind to causlality.  Its an interesting insight.

For an insight into my real interest please visit: www.mcgregorwinery.com
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Jean M
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« Reply #43 on: June 11, 2012, 02:01:15 PM »

Most of us are Partakers, although, there is some disagreement as to the original source of the name "Gregor", Giric, Gregory

"Partaker" I presume from the format of various Acts against the clans  "kin, men, servants and partakers" i.e. supporters. As you will know this does not imply any biological relationship closer than being human (and presumably Scottish).

I have already explained the source of the personal name. The Clan Gregor does not start with the first person in Scotland to be given the personal name Gregor. A whole lot of fable has evidently been grafted on to the true history of the clan named after Gregor of the Golden Bridles. Of course there were earlier persons called Gregor. That does not mean that they were related to Gregor of the Golden Bridles, any more than a person today in Illinois given the name Robert is automatically related to Robert the Bruce.

There are clearly several different families in Scotland which descended from a Gregor who happened to live at the time when the old patronymics of X mac Y were becoming hereditary.  

It would not be at all surprising to find a subset within the McGregor project which brings together men of a particular lineage going back to one of these Gregors, or even several such subsets - all completely unrelated to each other and the Ian Cam.
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« Reply #44 on: June 11, 2012, 02:11:04 PM »

....
I am not supporting Klyosov, I am simply evaluating/ showing what his technique for estimating longer periods of time results in....

That's fine that you don't support Klyosov's techniques, but then don't use them in your assertions as you did in this thread:


.... Can we create a new estimate of Hg age using this assumption.  For instance, I showed (having 8 mutations) that my haplotype is separated from M269/P25 by 40 K years.  Does that make any sense? ....

....How have you shown that your haplotype is separated from M269 or P25 by 40K years and which is it? M269 or P25?

If you accept Klyosovs assertions of his approach, then I have demonstrated that fact. ....

I'm a still a little confused about the MacGregor Ian Cam subgrouping...
For myself I have worked with Dr. Richard McGregor and Dr. Neil MacGregor on the MacGregor data set for almost five years.  We don't fully agree on everything but I think we have a common agreement on the Ian Cam and who the membership is. ...  

Perhaps you and he agree, but that doesn't mean membership indicates people that are related in some kind of historic timeframe.   Please consider asking the project admins to separate at least the Z253+ and 1039-A-Sc Scots folks and then the rest into different subgroupings. You might also consider de-emphasizing the importance of 391=10 except within subclades.

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« Reply #45 on: June 11, 2012, 04:17:27 PM »

But the STR diversity in western Europe is low. Genetic bottlenecks are supposed to account for that, and maybe they do, but they devastate the argument from modern frequency. I've said this elsewhere before, but it bears repeating. If R-M269 could recover from a bottleneck or series of bottlenecks so severe that it or they could create the "illusion" that R-M269 In Europe is much younger than it actually is, then the argument from frequency is gone. Whether R-M269 recovered after bottlenecks or arrived in Europe late, it's all the same: it achieved its success since that time and not as a consequence of steady, continuous growth since the Paleolithic or Mesolithic. So, an early arrival is either wishful thinking or a non sequitur.
ic or Paleolithic European R-M269 result. I'm betting that won't happen, however.
I don't agree with this reasoning because the population density in West Europe was not the same after the glacial peaks . In fact, the southern third part was populated weakily and the 2 northern third parts were empty totally, therefore the population  increase and extension didn't meet any human obstacle.
 For the Early Neolithic, it is difficult to say with what speed  Mesolithics succeeded to adapt to new economic conditions. In the European colonization, settlements succeeded to the detriment of local populations in Australia and part of America but also after some initiat success, failure to settle regions in Asia/Africa and populated agricultural regions of America,  he great  explanation for the removal of local populations in great regions of the world away from Eurasia/Africa with  no contact since dozens of millenia .

For Late neolithic and Chalcolithic, West Europe was already populated with several millions inhabitants and we have a lot of traces of dense and powerful  fortifications for this time and before,  and there was no technical  gap to allow newcomers to eliminate indigenes. In more, there is no archeological proof of their arrivals and if Bell Beakers were important for diffusion of some technics, the archeological density of BB sites must not be exagerated, very weak in a lot of regions. Even in regions described as Bell Beaker areas , find a BB tomb is a rare event.

Please, avoid to  reject any opposite  argument by invoking "wishful thinking". It is the best way to be blind.
  
« Last Edit: June 12, 2012, 02:07:30 AM by palamede » Logged

Y=G2a3b1a2-L497 Wallony-Charleroi; Mt=H2a2a1 Normandy-Bray
Dodecad-DiY: E Eur 9,25% W Eur 48,48% Med 28,46% W Asia 11,70%
World9: Atl-Balt 67,61% Southern 13,23% Cauc-Gedr 12,73%
K12a: North-E 39,71% Med 37,9% Cauc 12,55% Gedr 5,78% SW Asia 2,13%
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« Reply #46 on: June 11, 2012, 04:35:57 PM »

But the STR diversity in western Europe is low. Genetic bottlenecks are supposed to account for that, and maybe they do, but they devastate the argument from modern frequency. I've said this elsewhere before, but it bears repeating. If R-M269 could recover from a bottleneck or series of bottlenecks so severe that it or they could create the "illusion" that R-M269 In Europe is much younger than it actually is, then the argument from frequency is gone. Whether R-M269 recovered after bottlenecks or arrived in Europe late, it's all the same: it achieved its success since that time and not as a consequence of steady, continuous growth since the Paleolithic or Mesolithic. So, an early arrival is either wishful thinking or a non sequitur.
ic or Paleolithic European R-M269 result. I'm betting that won't happen, however.
I don't agree with this reasoning because the population density in West Europe was not the same after the glacial peaks . In fact, the southern third part was populated weakily and the 2 northern third parts were empty totally, therefore The population  increase and extension didn't meet any human obstacle.
 For the early neolithic, it is difficult to say with what speed  mesolithics succeeded to adapt to new economic conditions. In the European colonization, settlements in detriment   to local populations in Australia and part of America but after initial successes, it was a failure in a lot of regions. In more microbian stress was an important explanation for the removal of local populations in great regions of the world away from Eurasia/AFrica with  no contact since dozens of millenia .

For Late neolithic and Chalcolithic, West Europe was already populated with several millions inhabitants and we have a lot of traces of dense and powerful  fortifications for this time and before,  and there was no technical  gap to allow newcomers to eliminate indigenes. In more, there is no archeological proof of their arrivals and if Bell Beakers were important for diffusion of some technics, the archeological density of BB sites must not be exagerated, very weak in a lot of regions. Even in regions described as Bell Beaker areas , find a BB tomb is a rare event.

Please, avoid to  reject any opposite  argument by invoking "wishful thinking". It is the best way to be blind.

Palamede, some days I feel like I'm going blind and dumb (of the head) but I can not track your logic.

I understand that RMS is saying R1b's Western European frequencies can not be explained by an indigenous, Paleolithic population of R1b's. No matter whether R1b was Palolithic in Europe or not, there was some sort of bottleneck or complete lack of existence for R1b in Western Europe before a late (probably Neolithic or Bronze Age) growth spurt.

His logic is R1b existence before the bottleneck is no explanation for a current high frequency since the bottleneck essentially killed it (R1b) or at least it's diversity.  There had to be a late growth spurt for R1b, be it in situ (in place) or coming from the east.

Please correct me if I'm wrong, RMS, but I think I get what you are saying. I also don't think you are excluding a Neolithic expansion for R1b, although I'm not sure what Palamede is thinking on that.

Palamede, I don't understand your logic unless it is just that no one (R1b, nor anyone) could've expanded to such high frequencies from a Copper/Bronze Age or Neolithic beginning.  Is that it?

Remember, we are not talking about total population replacement, just paternal lineages.   Also bear in mind that Europe before the Copper/Bronze Ages (and for sure before the Neolithic) did not have metalurgy and did not have Indo-European languages nor horseback riding along with a few other things.
« Last Edit: June 11, 2012, 04:42:03 PM by Mikewww » Logged

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« Reply #47 on: June 11, 2012, 08:15:29 PM »

You're right, Mike, and I didn't understand what Palamede was saying either.

I don't believe R1b has been in Europe since the Paleolithic Period or even the Mesolithic, but the argument from modern frequency dies whenever the proponents of "old R1b" invoke bottlenecks to account for the lack of haplotype diversity.
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« Reply #48 on: June 12, 2012, 02:32:17 AM »

You're right, Mike, and I didn't understand what Palamede was saying either.

I don't believe R1b has been in Europe since the Paleolithic Period or even the Mesolithic, but the argument from modern frequency dies whenever the proponents of "old R1b" invoke bottlenecks to account for the lack of haplotype diversity.

In western European regions, there have been  a lot of big population decreases since Mesolithics to end of Middle Ages (The last important was Black Plague ) and therefore great removals of lineages which reduced haplotype diversity. It is useless and certainly wrong to postulate an enormous  bottleneck to reduce  population to one male   in Chalcolithic to be in accordance with your predicted datation and your silly certitude of a unique  man come from anywhere to replace 30 to 95% of the male population of Western Europe according to the regions, this occured 5.000 years ago when the following centuries give thousands  of sites prolonging the old cultures and traditions.

A replacement at the dawn of the Neolithic is more possible, but it was the time of the propagation of "Neolithic" haplogroups like E,G,J,T, later R1a with Corded Ware, which are found in settler skeletons along the Med coast and Germany. It would be difficult to a unique lineage of  R1b to dominate the other haplogroups and to stop their expansions.

I repeat there was no real important technical gap in Chalcolithics (only maybe an organisational and ideological gap in favour of the Indo-europeans). First horseback battles took place at the time of Neo-Assyrian empire (900-600BC),  first war chars dating of 1900-1700BC, first bronze arms in Near East from 2600BC, 2200BC in Western Europe, bronze swords from 1900-1700BC.

To make war tools, copper is nor better than flint. Even, flint daggers and flint arrow points were better and we know Late Neolithic populations (before Bell Beakers) were warriors and aggressive often. 
« Last Edit: June 12, 2012, 02:46:12 AM by palamede » Logged

Y=G2a3b1a2-L497 Wallony-Charleroi; Mt=H2a2a1 Normandy-Bray
Dodecad-DiY: E Eur 9,25% W Eur 48,48% Med 28,46% W Asia 11,70%
World9: Atl-Balt 67,61% Southern 13,23% Cauc-Gedr 12,73%
K12a: North-E 39,71% Med 37,9% Cauc 12,55% Gedr 5,78% SW Asia 2,13%
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« Reply #49 on: June 12, 2012, 07:54:13 AM »

You're right, Mike, and I didn't understand what Palamede was saying either.

I don't believe R1b has been in Europe since the Paleolithic Period or even the Mesolithic, but the argument from modern frequency dies whenever the proponents of "old R1b" invoke bottlenecks to account for the lack of haplotype diversity.

. . . your silly certitude . . .

Back off and grow up.

You misunderstood what I wrote, so don't tell me about my "silly certitude", because I am not certain about anything in this field.

Try reading what I wrote again . . . and again.

Maybe eventually you will understand it.

Here it is again, as simple as I can make it.

Advocates of "Paleolithic European R1b" or "Mesolithic European R1b" sometimes argue that R1b must have been in Europe since those periods because today there is so much R1b there. The idea is that it takes a long long time for a y haplogroup to achieve such dominance.

Okay, fine.

But the haplotype variance of R1b (R-M269 really) in Europe, especially western Europe, is relatively low. To explain that away, the advocates of Paleolithic or Mesolithic European R1b claim genetic bottlenecks must have greatly reduced or very nearly terminated the European R1b population, thereby reducing its diversity and making it appear much younger than it really is.

My point, which you are apparently missing, is this:

Whether R1b is less diverse in Europe because of bottlenecks or because it arrived there relatively late, it's all the same when it comes to modern frequency. As a consequence, modern frequency cannot be used as an argument for the great antiquity of R1b in Europe.

Get it?

R1b has achieved its position of European dominance either a) since a last serious bottleneck that occurred long after its first arrival, or b) since a more recent arrival that occurred about the same time as the bottleneck proposed by the advocates of position a.

Either way, it got as big as it has in Europe only since that time (i.e., the time of either the bottleneck or the arrival) and not in a steady, continuous progress since the Paleolithic or Mesolithic periods, even if it was in Europe that long ago.

That is why the modern frequency of R1b in Europe is not an argument for its antiquity there.
« Last Edit: June 12, 2012, 08:00:21 AM by rms2 » Logged

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