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Author Topic: The "randomness" of the STR Mutational process  (Read 2147 times)
palamede
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« Reply #50 on: June 13, 2012, 07:16:30 AM »

You are right probably and I am unable to understand the subtle depth of your reasoning.

Anyway, if we suppose the TMRCA of a clade is 5000BP calculated with the pedigree mutation rate, it seems for you there is only 2 possibilities  

1) If the first man with the mutation could be some generations older, the date (5000BP) is relative to the first  male common  ancestor of every tested people of the clade when we go to the past.

2) As this seems the case for I1 which TMRCA (with a lot of common SNPs to ever I1) is lot younger than I2 TMRCA which bloomed into surviving  branches  quickly, 5000 years ago, A bottleneck reduced the clade people to one or some males. But last I1 bottleneck is a lot sooner than 5000BP, certainly 10-12,000BP with the first populating of empty Scandinavia.

This 2 ways seems me impossible for different point of views : archeology (I explained you before) , anthropology (How do you explain the specific physical features and the autosomal components of the geographical ancesty) , prehistorical demography (it cannot know the modern growth rate , epidemic, childish mortality, economic  pressure of neighbouring populations, local wars, inevitable mixing of joint populations weakly physicaly differenciated, non-paternal events  and so on ) . We must go by an other way.

I guess an other way, but I have not got the competence to decide if it is valid for the point of view of genetic stastistics.

I believe, but I am not sure the used methodes to  calculate the MRCA by number of generations depends on the hypothesis that the clade population, was a slow, steady and quiet growth to reach the present population size of the clade from the MRCA.
The other way is the clade would have several bottlenecks (by wars, starvations, climate changes or epidemics)  reducing the population, firstly from thousands  to some hundred people, later from dozens of thousands  to some thousand people and finally in protohistorical and historical times the clade was reduced by a quarter or a third or an half or more of the population by events like  the Justinian plague (550ad an later) or the Black Plague (1350 ad and later) and their recurrences each generation during one or two centuries  for the last catastrophs.
These events caused the removals of a great part of the lineages thru the ages with the help of the laws of the genetic drift which occurs the  disappearance of the more fragile lineage, this   involved great loss of the genetic diversity, therefore great consequense for the result of the calculation of the MRCA and TMRCA.

In more, if you are interested by the history of nobility families, you should see we mustn't exagerate the quality of  their demography. A lot of male branches disappeared thru the times, even when they can legitimate the bastards, as in Spain or Italy.

All these withouttaking in to account the quality of the "randomness" of the STR Mutational process.
« Last Edit: June 13, 2012, 08:40:40 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%
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rms2
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« Reply #51 on: June 13, 2012, 09:13:16 PM »

You are still missing the point or choosing to miss it.

I never said bottlenecks are or were impossible or that they never occurred.

I simply said that one cannot reasonably argue that the high modern frequency of R-M269 in western Europe is evidence that it arrived there very early (i.e., in the Paleolithic or Mesolithic period) and then turn around and explain away its relatively low haplotype diversity by means of genetic bottlenecks.

If R-M269 could advance to its present dominance since the last severe bottleneck, it could also advance to its present dominance if it had only just arrived at about that same time. If it had x years to achieve dominance, then it had x years to achieve dominance, whether those years span the time from the last bottleneck or from the date of its arrival.

So, you see, the high modern frequency of R-M269 in much of Europe is not evidence that R-M269 got there in the Paleolithic or Mesolithic Period. There may be some other types of indications that it did (none that I find compelling), but high modern frequency is not one of them.
« Last Edit: June 13, 2012, 09:19:24 PM by rms2 » Logged

palamede
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« Reply #52 on: June 15, 2012, 05:47:51 AM »

You are still missing the point or choosing to miss it.

I never said bottlenecks are or were impossible or that they never occurred.

I simply said that one cannot reasonably argue that the high modern frequency of R-M269 in western Europe is evidence that it arrived there very early (i.e., in the Paleolithic or Mesolithic period) and then turn around and explain away its relatively low haplotype diversity by means of genetic bottlenecks.

If R-M269 could advance to its present dominance since the last severe bottleneck, it could also advance to its present dominance if it had only just arrived at about that same time. If it had x years to achieve dominance, then it had x years to achieve dominance, whether those years span the time from the last bottleneck or from the date of its arrival.

So, you see, the high modern frequency of R-M269 in much of Europe is not evidence that R-M269 got there in the Paleolithic or Mesparizonolithic Period. There may be some other types of indications that it did (none that I find compelling), but high modern frequency is not one of them.
Amen

If the intraclade calculation cannot escape from the loss of diversity due to the removal of the lineages causing by the genetic drift, specially during the successive  bottlenecks of variable intensity. I would like to learn more how the interclade method was susceptible or not to the bottlenecks suffered by the clades used for the comparison.

edit: Sorry, I wanted to write "interclade" and not  "intraclade". I corrected.
« Last Edit: June 15, 2012, 05:07:06 PM 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%
Mike Walsh
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« Reply #53 on: June 15, 2012, 05:47:54 PM »

You are still missing the point or choosing to miss it.

I never said bottlenecks are or were impossible or that they never occurred.

I simply said that one cannot reasonably argue that the high modern frequency of R-M269 in western Europe is evidence that it arrived there very early (i.e., in the Paleolithic or Mesolithic period) and then turn around and explain away its relatively low haplotype diversity by means of genetic bottlenecks.

If R-M269 could advance to its present dominance since the last severe bottleneck, it could also advance to its present dominance if it had only just arrived at about that same time. If it had x years to achieve dominance, then it had x years to achieve dominance, whether those years span the time from the last bottleneck or from the date of its arrival.

So, you see, the high modern frequency of R-M269 in much of Europe is not evidence that R-M269 got there in the Paleolithic or Mesparizonolithic Period. There may be some other types of indications that it did (none that I find compelling), but high modern frequency is not one of them.
Amen

If the intraclade calculation cannot escape from the loss of diversity due to the removal of the lineages causing by the genetic drift, specially during the successive  bottlenecks of variable intensity. I would like to learn more how the interclade method was susceptible or not to the bottlenecks suffered by the clades used for the comparison.

edit: Sorry, I wanted to write "interclade" and not  "intraclade". I corrected.

As far I know, Ken Nordtvedt is the inventor of interclade TMRCA calculations.  You can read about it, look at his concept formulas and graphics and then download the spreadsheet implementation here:
http://knordtvedt.home.bresnan.net/
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JeanL
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« Reply #54 on: June 19, 2012, 11:38:16 AM »

I have been reading this study written by John H Gillespie, and I think it would be something to examine closely when it comes to assuming randomness in the mutational process.

Genetic Drift in an Infinite Population: The Pseudohitchhiking Model

Quote from: Gillespie.et.al.2000

Selected substitutions at one locus can induce stochastic dynamics that resemble genetic drift at a closely linked neutral locus. The pseudohitchhiking model is a one-locus model that approximates these effects and can be used to describe the major consequences of linked selection. As the changes in neutral allele frequencies when hitchhiking are rapid, diffusion theory is not appropriate for studying neutral dynamics. A stationary distribution and some results on substitution processes are presented that use the theory of continuous-time Markov processes with discontinuous sample paths. The coalescent of the pseudohitchhiking model is shown to have a random number of branches at each node, which leads to a frequency spectrum that is different from that of the equilibrium neutral model. If genetic draft, the name given to these induced stochastic effects, is a more important stochastic force than genetic drift, then a number of paradoxes that have plagued population genetics disappear.

« Last Edit: June 19, 2012, 11:41:38 AM by JeanL » Logged
ironroad41
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« Reply #55 on: June 19, 2012, 01:20:32 PM »

I have been reading this study written by John H Gillespie, and I think it would be something to examine closely when it comes to assuming randomness in the mutational process.

Genetic Drift in an Infinite Population: The Pseudohitchhiking Model

Quote from: Gillespie.et.al.2000

Selected substitutions at one locus can induce stochastic dynamics that resemble genetic drift at a closely linked neutral locus. The pseudohitchhiking model is a one-locus model that approximates these effects and can be used to describe the major consequences of linked selection. As the changes in neutral allele frequencies when hitchhiking are rapid, diffusion theory is not appropriate for studying neutral dynamics. A stationary distribution and some results on substitution processes are presented that use the theory of continuous-time Markov processes with discontinuous sample paths. The coalescent of the pseudohitchhiking model is shown to have a random number of branches at each node, which leads to a frequency spectrum that is different from that of the equilibrium neutral model. If genetic draft, the name given to these induced stochastic effects, is a more important stochastic force than genetic drift, then a number of paradoxes that have plagued population genetics disappear.


I forwarded your reference to Dr. Neil MacGregor, biochemist, for his opinion.  The last time I had correspondence with Mike Weale, he felt that understanding linkage disequilibrium was important.  This is not my field so I can add little.

From a perspective of the probability of a mutational event, it is a "black swan" as I mentioned elsewhere.  Its out of the 3 sigma range of probabilities, so I don't know how to describe the space known as extremistan (term coined by  N. Taleb).  The fact that we can have multisteps also negates a simple gaussian model.

Right now, as I mentioned in an entry on another thread, I am concerned about the properties of the databases we have to work with.  They are highly correlated and its not clear to me, without a lot cherrypicking, how we can sensibly extract TMRCA data?  As I've said many times, the few sets of data I have been able to analyze and verify, I had to be very careful with unique mutational events and only use independent entries.  As best as I understand it the mutational process has yet to be correctly modelled?
« Last Edit: June 19, 2012, 01:22:03 PM by ironroad41 » Logged
JeanL
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« Reply #56 on: June 19, 2012, 01:32:28 PM »

I think there is a whole lot of sampling error going on when one works with the FTDNA databases.
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