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Author Topic: STR Wars: Is diversity meaningful? more meaningful than Hg frequency?  (Read 17386 times)
JeanL
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« Reply #275 on: July 11, 2012, 01:56:56 PM »

Yes, slow markers are more stable. That is essentially by definition.

Well, yeah, in fact they are slow markers, because they are regions in the Y-Chromosome less prone to slippage, thus they are more stable. So them being more stable is what makes them slow markers.

By "washing out" I just mean that the more data you have, generally, abberations do not significantly impact the final estimates.

Well bigger sample size in terms of population can only do good, so yeah, more data is generally better.

Yes, I agree that we should deselect STRs that do not have a linear relationship with time for the duration in question.  The problem is figuring out which to deselect. It isn't necessarily the fast ones. There is some work that problems occur at higher allele value STRs. The only deselections that I have rationale for are multi-copy ones, null cases and then the research that Marko Heinilla did.

There is yet another problem, which I recently started pondering about, and under a Wright-Fisher expansion model would definitely posit a problem, at least theoretically, and that is that if the TMRCA of a given population is older than the “time to fixation/reaching majority frequency” of a given STR, then it would yield the erroneous modal value, and thus cause the estimates to appear much younger than they should. I have started running simulations about it, but I would have to run a significant number of simulations before any meaningful result is produced, in the mean time, what I have observed is that when the TMRCA is 5 folds the time to majority of an STR, then the effects are immediate, and they are observable even within a few simulations. Marko H research that has thus far been presented here has nothing to do with modal values, I believe he was observing the relationship between repeat number and mutation rates, as well as the range of observed alleles and mutation rates. The effect of what I am talking about would actually manifest itself as a difference of probably 3 to 5 folds in the TMRCA when calculating it using a set of slow markers vs. a set of fast markers.  Essentially, if proven true, it means that the there is no way to calculate the putative ancestral allele value of fast markers, if the MRCA occurred at a time earlier than 1/μ generations, where μ is the mutation rate of the STR.
« Last Edit: July 11, 2012, 01:58:30 PM by JeanL » Logged
ironroad41
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« Reply #276 on: July 15, 2012, 02:07:00 PM »

Are there any scientific papers out there that use or show different Y DNA STR mutation rates for different haplogroups?

I don't know if there are any  papers out there, but I have been studying the  yfreq database at ancestry.com: www.freepages.genealogy.rootsweb.ancestry.com/~geneticgenealogy/yfreq.htm and have extracted some information which may apply here.  First a question about the word diversity in the Y STR context.  Is it simply the reduction in the modal value or is it the spread of the distribution.  I make that distinction since many mutations are about the modal and back mutations are prevalent, possibly preserving  the modal value.  In any case, I try to look at both criteria where possible.
 
I've reached several conclusions: 1. Diversity is not a measure of age since mutation rate varies with modal value, independent of Hg, for a dys loci.  2. This leads me to conclude that using the same mutation rates for all Hgs is in error since they don't all have the same modal values.  3. High off modal values may be due to the fact that a mutation occurred near the time of the founder and fixation occurred.

data:  look at 390 in the data set, especially hg E3a with a modal of 21 and 91% value. It has the smallest diversity of all 7 hgs presented.  The next lowest is G with a modal at 22 and 75%.  All the remaining hgs have higher modals.  Given that E3a is older or at least as old as the other hgs, I conclude that the modal value is the issue.  391 is a similar example with R1b having the highest modal value 11 at a (67%) value.  Consider 426 in which the first 5 hgs have a modal value of 11 and all have about 99%+ values.  R1a and R1b have a modal of 12 and a very slightly lower value (99,98). Finally look at 388. Ea,b, R1a,b all have modals of 12 (note that R1a must have had a multistep to 10).  The oddballs in this set are G with 50% at 12 and 50% at 13 and then we have I and J2.  I has a modal at 14 (56%) and J has a modal at 15 (71%).  Applying R1b derived rates to these hgs would significantly affect the variance estimate for this locus.

To me the message is clear; there is a lot more complexity in this process than we are currently accounting for and diversity has limited application in describing this process.  JMHO

edit:  I have found another leo little web page, which expresses the above comments quite vividly. It is at the same site above and presents the genetic diversity as a function of dys loci over the same 7 Hgs.  It clearly presents the random variability in gene diversity from locus to locus.
« Last Edit: July 15, 2012, 02:30:42 PM by ironroad41 » Logged
ironroad41
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« Reply #277 on: July 19, 2012, 01:54:31 PM »

I was hoping to generate some discussion on Leo Littles work on gene diversity.  His data presents clearly that diversity and age are not synonymous.  My impression is that there is a sensitivity of mutation rate to allele value,  lower values usually having lower rates.

I believe it is critical to our understanding of relative ages of Hg's, where there are small but important changes in the modal value.

Is there some other interpretation we can give to Leo's data?  I'd like to hear about it.
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Mike Walsh
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« Reply #278 on: September 14, 2012, 08:32:27 AM »

I copied this from another thread so as not to distract from it.

....
And let me just say....  Y-DNA STRs are so old school.
...

What do you mean by that? The use of Y DNA STRs in understanding paternal lineages in both genetic genealogy and population genetics has been very helpful. They are no panacea for the world's ills but another source of data related to genetics that is sorely needed.
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acekon
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« Reply #279 on: September 21, 2012, 10:58:29 AM »

Using str's as a supplement is one thing. Mapping variance in 9 str's and making broad assumptions, and then asking for samples of Z2105+/-  in the same breath is quite simply a paradox.
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« Reply #280 on: September 21, 2012, 11:09:18 AM »

Using str's as a supplement is one thing. Mapping variance in 9 str's and making broad assumptions, and then asking for samples of Z2105+/-  in the same breath is quite simply a paradox.

I agree, except for the part of Z2105 and a paradox. I'm not sure what you are talking about on that piece.
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Mike Walsh
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« Reply #281 on: October 01, 2012, 04:56:42 PM »

Haplotype diversity does not equall origin. If you want proof of that then study any of the private SNPs and their modal haplotypes.Modal haplotype and SNP go hand in hand. If you make the assumption that we are all descended from a single SNP like U106 then you have to think that at one time U106 was a private one.So you will all find the answers that you are looking for by studying them. This is only my opinion.

I copied this over from the IE mapping thread because it could take that conversation off track.

I do not think haplotype diversity equals origin, but I think it can be indicator of direction of movement, and is more useful than frequency for indicating that.

I do not see proof how private SNPs and modal haplotypes prove (you use the word "proof") what you are saying. Please explain.
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stoneman
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« Reply #282 on: October 02, 2012, 03:44:31 AM »

A modal haplotype is formed from the majority of people having a certain set of ystr values. Majority always rules. The modal also shows which SNP the group belongs to and suggests it is ancestral for that group. I have studied thousands of haplotypes at ysearch over the last six years.I found the markers for the Clan Colla group and it took me months to convince some of them. Now I can identify the whole group with one marker. I can identify the specific markers for some other subclades. The L1 group can be identfied with one marker as well.

A portion of this message was deleted.  Terry
« Last Edit: October 02, 2012, 12:00:31 PM by Terry Barton » Logged
Mike Walsh
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« Reply #283 on: October 02, 2012, 11:28:55 AM »

A modal haplotype is formed from the majority of people having a certain set of ystr values. Majority always rules. The modal also shows which SNP the group belongs to and suggests it is ancestral for that group. I have studied thousands of haplotypes at ysearch over the last six years.I found the markers for the Clan Colla group and it took me months to convince some of them. Now I can identify the whole group with one marker. I can identify the specific markers for some other subclades. The L1 group can be identfied with one marker as well.

I agree with you in that a mode is a statistical concept that most common value (not necessarily majority, though) of a particular characteristic (STR in this case) within a population.

I agree with you that the modal haplotype only suggests or indicates an ancestral value. We don't really know nor can't know the ancestral values without digging up bones for the ancestor.

Sometimes there are correlations of STR markers to SNPs but this is not solid, 100% accurate. For example, U106+ people typically have 492=13 and P312+ rarely do, but there are P312+ people that are 492=13 and one higher, even 492=14.

A portion of this massage was deleted.  Terry

I know you said that diversity does not equal origin. I agree, they definitely don't equal, but I still think diversity is useful for ascertaining age and can be indicative for direction back to the origin. I don't see anything in your discussion where you explain why that isn't true.  Please explain.
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stoneman
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« Reply #284 on: October 02, 2012, 01:42:34 PM »

Lets assume that U106 is 6000 ybp. There is a U106 man from Cornwall who has a gd of 6 from the U106 Modal and I have 16 from the modal. Between us there are 22.The age of U106 does not change. Another example another man here in Ireland is a gd of 25 from the modal and I am 16 from the modal and we have a gd of 41 between us and the age of U106 stays the same. If I say to you that U106 originated in Ireland what will you say? Diversity equals origin.
I have looked at a few private or family SNPs and haplotypes and I have a better understanding of things.That is how all of these major subclades started. You are the person that states often that we are all descended from one R1b-L11 man.
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Mike Walsh
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« Reply #285 on: October 02, 2012, 04:50:39 PM »

I've reversed the order of your post so I can respond to the clearer stuff first.

I have looked at a few private or family SNPs and haplotypes and I have a better understanding of things.That is how all of these major subclades started. You are the person that states often that we are all descended from one R1b-L11 man.

Yes, we think that the mutation L11 (aka S127) is a UEP (Unique Event) type SNP. In other words, it happened only once in the lineage of all R1b people. Therefore, it follows that any subclade, marked by an SNP that descends from the L11 family, has a single common ancestor. Essentially, its by definition of phylogenetic tree that there was one man that was the most recent man from which all existing P312, U106 and L11* descend from.

The same can be said for U106. The U106 (aka S21) mutated only once and is carried on to all of the Y descendants of that man.  We also know that this U106 man can't be older than the most recent common ancestor for all of U106 and P312.

Lets assume that U106 is 6000 ybp. There is a U106 man from Cornwall who has a gd of 6 from the U106 Modal and I have 16 from the modal. Between us there are 22.The age of U106 does not change. Another example another man here in Ireland is a gd of 25 from the modal and I am 16 from the modal and we have a gd of 41 between us and the age of U106 stays the same. If I say to you that U106 originated in Ireland what will you say? Diversity equals origin.

I agree that the age of the first U106 man is what it is.

You can say U106 originated in Ireland and here's my response. I don't know where the first very first U106 man originated. I don't think we can ever know. So you see, my answer was not "diversity equals origin."

If you ask in what directions from where U106 expanded to its current positions, I can give you opinions on that based on diversity of STRs, SNPs (notice I didn't say just STRs), relatives of U106 (such as brothers like P312 and L11*, cousins like L51*, sons like Z381, etc.), and in the context of cultural and linguistic knowledge.  We probably need to look hard at very distant relatives that might have cohabitated as well, such as I1, R1a1, etc.  as well as correlations with mt DNA.

I'm not following your proof, though.
Haplotype diversity does not equall origin. If you want proof of that then study any of the private SNPs and their modal haplotypes

Are you saying gene diversity has no relationship to time, i.e., the number of generations back to a common ancestor? The difference between a modal haplotype and an ancestral haplotype doesn't change the concept of mutations accumulating over the generations.
« Last Edit: October 02, 2012, 05:03:00 PM by Mikewww » Logged

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Jarman
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« Reply #286 on: October 02, 2012, 05:09:46 PM »

Lets assume that U106 is 6000 ybp. There is a U106 man from Cornwall who has a gd of 6 from the U106 Modal and I have 16 from the modal. Between us there are 22.The age of U106 does not change. Another example another man here in Ireland is a gd of 25 from the modal and I am 16 from the modal and we have a gd of 41 between us and the age of U106 stays the same. If I say to you that U106 originated in Ireland what will you say? Diversity equals origin.

The age of U106 does not change but their TMRCA certainly are different.  Neither calculation would tell us anything about the populations' diversity in Cornwall or Ireland or Antarctica.
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Mike Walsh
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« Reply #287 on: October 02, 2012, 05:50:13 PM »

I tried to add this in the "personal attacks" thread but no replies are allowed there.

....
A portion of this massage was deleted.  Terry

I see Terry deleted two sentences here. He certainly has the right to do so. I just want to be clear everyone I used no obscenities and did not personally attack anyone. I guess Terry just wants to make sure that element of that conversation has stopped, which I agree with and I proactively support Terry in this effort.
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stoneman
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« Reply #288 on: October 02, 2012, 05:58:00 PM »

I didnt say that U106 originated in Ireland but I can say that some subclades or SNPs did. Its the same with all the haplogroups that are found here.
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stoneman
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« Reply #289 on: October 03, 2012, 12:43:21 PM »

Lets assume that U106 is 6000 ybp. There is a U106 man from Cornwall who has a gd of 6 from the U106 Modal and I have 16 from the modal. Between us there are 22.The age of U106 does not change. Another example another man here in Ireland is a gd of 25 from the modal and I am 16 from the modal and we have a gd of 41 between us and the age of U106 stays the same. If I say to you that U106 originated in Ireland what will you say? Diversity equals origin.

The age of U106 does not change but their TMRCA certainly are different.  Neither calculation would tell us anything about the populations' diversity in Cornwall or Ireland or Antarctica.

How can one man have six mutations in 6000 years and two others have sixteen and twenty five in the same time frame?Is this the wrong modal for U106(HXTNR).Shouldnt everyone have the same gd from a modal haplotype?How did you guys work out a TMRCA for U106?
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Mark Jost
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« Reply #290 on: October 03, 2012, 01:58:27 PM »

Lets assume that U106 is 6000 ybp. There is a U106 man from Cornwall who has a gd of 6 from the U106 Modal and I have 16 from the modal. Between us there are 22.The age of U106 does not change. Another example another man here in Ireland is a gd of 25 from the modal and I am 16 from the modal and we have a gd of 41 between us and the age of U106 stays the same. If I say to you that U106 originated in Ireland what will you say? Diversity equals origin.

The age of U106 does not change but their TMRCA certainly are different.  Neither calculation would tell us anything about the populations' diversity in Cornwall or Ireland or Antarctica.

How can one man have six mutations in 6000 years and two others have sixteen and twenty five in the same time frame?Is this the wrong modal for U106(HXTNR).Shouldnt everyone have the same gd from a modal haplotype?How did you guys work out a TMRCA for U106?

Isogg has a great line concerning your First and Third question.
http://www.isogg.org/wiki/Most_recent_common_ancestor

"Even though each living person receives genes (in original or mutated forms) in dramatically different proportions from these ancestors from the identical ancestors point,[5] from this point back all living people share exactly the same set of ancestors,..."

I just ran U106 all 111 markers from a list I had in August of 320 HTs .

YrsPerGen=30

IntraClade Coalescence Age
Generations    StdDevInGen   YBP    +-YBP    VARP    SD   

105.8   21.2   3,173.4   636.3   24.873   4.987

Founder's Age
Generations   StdDevInGen   YBP  +-YBP   Max   VAR   SD
106.1   21.2   3,183.3   637.3   3,820.6   24.951   4.995

Using 111 markers has been showing 10-20 generations (300-600 YBP) less than what 67 markers will show.

MJost
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Neg: DF23 L513 L96 L144 Z255 Z253 DF21 DF41 (Z254 P66 P314.2 M37 M222  L563 L526 L226 L195 L193 L192.1 L159.2 L130 DF63 DF5 DF49)
WTYNeg: L555 L371 (L9/L10 L370 L302/L319.1 L554 L564 L577 P69 L626 L627 L643 L679)
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« Reply #291 on: October 03, 2012, 03:49:26 PM »

Lets assume that U106 is 6000 ybp. There is a U106 man from Cornwall who has a gd of 6 from the U106 Modal and I have 16 from the modal. Between us there are 22.The age of U106 does not change. Another example another man here in Ireland is a gd of 25 from the modal and I am 16 from the modal and we have a gd of 41 between us and the age of U106 stays the same. If I say to you that U106 originated in Ireland what will you say? Diversity equals origin.

The age of U106 does not change but their TMRCA certainly are different.  Neither calculation would tell us anything about the populations' diversity in Cornwall or Ireland or Antarctica.

How can one man have six mutations in 6000 years and two others have sixteen and twenty five in the same time frame?Is this the wrong modal for U106(HXTNR).Shouldnt everyone have the same gd from a modal haplotype?How did you guys work out a TMRCA for U106?

Everyone should not have the same GD from the ancestral haplotype. It is by chance that we end up where we are.

I like to envision a branching tree.


Some branches grow almost straight up but end up with smaller branches and twigs spreading to the side. Other branches shoot out to the side initially but some of their descendant branches grow back up. I don't think the actual Y DNA tree is nice and round though. Some major limbs probably died and fell away. Other branches grew faster.
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« Reply #292 on: October 04, 2012, 01:43:42 PM »

I'm just cataloging this post here so we don't lose it.
Quote from:  Vincent Vizachero
I think that David's question is whether there is evidence that haplogroups have been shown to have different mutation rates. The number of samples that would be required to produce such evidence is huge: way beyond the number collected for any study to date.
http://archiver.rootsweb.ancestry.com/th/read/GENEALOGY-DNA/2012-10/1349347745

My comments are that we how we are planning to apply STR mutation rates. Since we are using them to estimate ages, etc. what we care about is the expected mutation rate, not necessarily the observed rates.

I don't know of any reason to think that Y STR mutations are biologically linked to Y SNP mutations.  Does anyone?  If not, we should not expect mutation rates to be different by SNP based haplogroup within our species.  You could think of it as we are more alike than we are different.

While it is true that different markers have different rates, and that even a single marker has a different probability of mutating depending on its original value, the number that matters is the sum of mutation rates for all markers tested.

Quote from:  Vincent Vizachero
When you are testing 37 or 67 markers, it may be that one haplogroup has a higher modal value for marker A than another haplogroup. But if it has a lower modal value for marker B, the effect of allele length cancels out to some degree.

Over even just 37 markers, haplogroups have an average allele length that varies by only 1-2%: not enough to produce a significant difference in mutation rate.

I think you can see why Ken Nordtvedt says each STR is like a separate experiment and the more experiments you conduct the more reliable your aggregate results will be.

Translation: Long haplotypes are much better than short/bikini haplotypes for analysis. (EDIT: I meant for statistical analysis and the like, the more STRs, the better. Of course, a key off-modal STR might be critical for identifying potential matches.)
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stoneman
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« Reply #293 on: October 04, 2012, 03:26:35 PM »

If a man is predicted R1b and he has a null value at 439 then I could find all of them with just that one marker at ysearch if I wanted. . So ydna is a powerfull tool. One can tell a lot with bikini haplotypes.
Furthermore, there is a link between modal haplotype and SNP.
Ken N may be a genious and others too but  we dont have to give them a blank check.We have the right to question everything  and there are lots of them that I could ask. After all it is my dna and my identity that he refers to when he mentions anything about U106.
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« Reply #294 on: October 05, 2012, 12:21:28 PM »

This is a quote from Anatole Klyosov in the same Rootsweb thread as the below.
Quote from: Anatolke Klyosov
... The above question was repeated and answered here dozens of times. In fact, the same mutation rate constants are fully applicable to all and any haplogroups. Lately, this issue was analyzed in details using thousands of haplotypes from various haplogroups. See the paper "Mutation rate constants in DNA genealogy (Y chromosome)". Adv. Anthropol., 2011, v. 1, No. 2, pp.
26-34.
http://www.scirp.org/journal/aa/
http://archiver.rootsweb.ancestry.com/th/read/GENEALOGY-DNA/2012-10/1349429460

----------------------------------------------------
I'm just cataloging this post here so we don't lose it.
Quote from:  Vincent Vizachero
I think that David's question is whether there is evidence that haplogroups have been shown to have different mutation rates. The number of samples that would be required to produce such evidence is huge: way beyond the number collected for any study to date.
http://archiver.rootsweb.ancestry.com/th/read/GENEALOGY-DNA/2012-10/1349347745

My comments are that we how we are planning to apply STR mutation rates. Since we are using them to estimate ages, etc. what we care about is the expected mutation rate, not necessarily the observed rates.

I don't know of any reason to think that Y STR mutations are biologically linked to Y SNP mutations.  Does anyone?  If not, we should not expect mutation rates to be different by SNP based haplogroup within our species.  You could think of it as we are more alike than we are different.

While it is true that different markers have different rates, and that even a single marker has a different probability of mutating depending on its original value, the number that matters is the sum of mutation rates for all markers tested.

Quote from:  Vincent Vizachero
When you are testing 37 or 67 markers, it may be that one haplogroup has a higher modal value for marker A than another haplogroup. But if it has a lower modal value for marker B, the effect of allele length cancels out to some degree.

Over even just 37 markers, haplogroups have an average allele length that varies by only 1-2%: not enough to produce a significant difference in mutation rate.

I think you can see why Ken Nordtvedt says each STR is like a separate experiment and the more experiments you conduct the more reliable your aggregate results will be.

Translation: Long haplotypes are much better than short/bikini haplotypes for analysis. (EDIT: I meant for statistical analysis and the like, the more STRs, the better. Of course, a key off-modal STR might be critical for identifying potential matches.)
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« Reply #295 on: October 06, 2012, 04:56:10 PM »

Mike,

I assumed you used MarkoH's Up/downMutationRatesRatio paper and his range of accuracy of the linear and quadratic models sheet to remove those STRs 7K ybp and under, along with removing the Multi-copy markers? Did you make some substitutions for a specific reason?

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« Reply #296 on: October 08, 2012, 12:30:00 PM »

I assumed you used MarkoH's Up/downMutationRatesRatio paper and his range of accuracy of the linear and quadratic models sheet to remove those STRs 7K ybp and under, along with removing the Multi-copy markers? Did you make some substitutions for a specific reason?

Reply #146 of this thread as the output of Marko Heinilla's linear duration assessment of FTDNA's first 67 STRs. http://www.worldfamilies.net/forum/index.php?topic=10513.msg130009#msg130009
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« Reply #297 on: October 08, 2012, 12:37:38 PM »

I'm just cataloging this here. It's a comment/post from a person who is an actuary.

Quote from: Sandy Paterson
... A mode is not used to calculate a mutation rate. The number of mutations are observed (6) and divided by the number of meioses (14,553). That gives .0004123 which is what they report. It really doesn't bother me how many mutated off 14 compared to how many mutated off 13 and so on.

There is some evidence presented by Ballantyne (I think it was) that the number of repeats provided a partial explanation for variance in mutation rates. I checked their work and found that it added hardly anything to R-squared.
http://archiver.rootsweb.ancestry.com/th/read/DNA-R1B1C7/2012-10/1349710154

Sandy is also the guy who says we want at least 50 STRs in our calculations. My reaction is that we should not remove STRs from our calculations unless we have good reason to do so. Everyone seems to agree that multi-copy markers can cause problems. In addition, there is no doubt that some STRs (apparently the ones with high repeats) reach saturation levels but where is the line drawn?  I'm not sure, but I feel pretty good about using the 36 markers that have the longer linear durations according to Heinilla. They seem to work in terms of consistency in comparing one haplogroup to another.
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R1b-L21>L513(DF1)>L705.2
Mark Jost
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« Reply #298 on: October 08, 2012, 01:46:50 PM »

I assumed you used MarkoH's Up/downMutationRatesRatio paper and his range of accuracy of the linear and quadratic models sheet to remove those STRs 7K ybp and under, along with removing the Multi-copy markers? Did you make some substitutions for a specific reason?

Reply #146 of this thread as the output of Marko Heinilla's linear duration assessment of FTDNA's first 67 STRs. http://www.worldfamilies.net/forum/index.php?topic=10513.msg130009#msg130009
Ah,  I forgot this old post. Its a little different than the page Marko recently sent me which I compared using his Linear YBP column.

https://dl.dropbox.com/u/50201824/old/timevaluesEtc/updownratio.html

and a link to his linear page for the above page.

"and the range of accuracy of the linear and quadratic models, the results are given here. "

https://dl.dropbox.com/u/50201824/old/timevaluesEtc/variance2.html

MJost
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148326
Pos: Z245 L459 L21 DF13**
Neg: DF23 L513 L96 L144 Z255 Z253 DF21 DF41 (Z254 P66 P314.2 M37 M222  L563 L526 L226 L195 L193 L192.1 L159.2 L130 DF63 DF5 DF49)
WTYNeg: L555 L371 (L9/L10 L370 L302/L319.1 L554 L564 L577 P69 L626 L627 L643 L679)
Mike Walsh
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« Reply #299 on: October 09, 2012, 12:21:30 AM »


Thanks, Mark. Do you have this document in a spreadsheet or CSV format?
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