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Author Topic: STR Wars: Is diversity meaningful? more meaningful than Hg frequency?  (Read 18540 times)
eochaidh
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« Reply #25 on: April 13, 2012, 05:11:18 PM »

The point I'm trying to make is that I have never even see a spot that has a higher diversity AND a higher frequency, even within L21+ or a subclade of L21+.

For isntance, a made up example: Lx+ is highest in Ireland #1, Scotland #2, Wales #3, England #4, France #5, Germany #6, but the diversity of Scotland #2 is higher than the diversity in Germany#6.

It seems that "low frequency equals high diversity" and "high frequency equals low diversity". If this is the case, then either we have an amazing mathematical coincidence or something is wrong.

Does it mean that a SNP originates in an area then the descendants ALWAYS go to a new area and prosper. Leaving the highest diversity in the lowest area of frequency.
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Mike Walsh
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« Reply #26 on: April 13, 2012, 05:27:20 PM »

The point I'm trying to make is that I have never even see a spot that has a higher diversity AND a higher frequency, even within L21+ or a subclade of L21+.

For isntance, a made up example: Lx+ is highest in Ireland #1, Scotland #2, Wales #3, England #4, France #5, Germany #6, but the diversity of Scotland #2 is higher than the diversity in Germany#6.

It seems that "low frequency equals high diversity" and "high frequency equals low diversity". If this is the case, then either we have an amazing mathematical coincidence or something is wrong.

Does it mean that a SNP originates in an area then the descendants ALWAYS go to a new area and prosper. Leaving the highest diversity in the lowest area of frequency.
I think, as has been pointed out, U152 may be a good example.  

L226 could be a case under L21.  I was about to say M222, but I actually get M222 with higher diversity in England... however, the STR variance differences on M222 are too close to say anything conclusively.

L21's history/prehistory may be different than U152.  Perhaps that is the story.

You should probably read the two studies on "Surfing the Wave". I think Klopfstein was the primary author.  I've pointed to them before.  No one is saying that concept always applies, just that it may apply in some situations.
« Last Edit: April 13, 2012, 05:36:33 PM by Mikewww » Logged

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« Reply #27 on: April 13, 2012, 05:29:26 PM »

Are there any scientific papers out there that use or show different Y DNA STR mutation rates for different haplogroups?
I can not locate one right now but I do recall the hypothesis in at least one paper.   The only one I can show you is that there is a difference between closely related species.

http://www.genetics.org/content/168/1/383.full.pdf+html

chimps vs. people may be too many generations apart, and this study was not Y DNA specific but it does support the concept.  

Does someone have a link to a DNA mutation rates for "family groups" paper?  I believe that was the topic, my google skill has failed me so it may have been an offline paper.

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eochaidh
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« Reply #28 on: April 13, 2012, 05:41:01 PM »

It just seems that a person could say that with L21 and its subclades, "Higher Frequency" will equal "Lower Diversity" and that person would be correct.

When I see someone bring up "Diversity" with L21 and/or its Subclades I think, "Why read it?" I know that the place of Highest Frequency has no chance of being the place of Highest Diversity. Which means that in EVERY case the descendants of the first man with a mutated SNP ALWAYS left the area of origin and prospered elsewhere. As a matter of fact, wherever they prospered the most, that place will be the place of Lowest Diversity.

So, when there is one L226 found on the Continent, or even in Britain L226's origin will move out of Ireland because Ireland, as the place of Highest Frequency, cannot be the place of Highest Diversity. I say this with 100% certainty.

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« Reply #29 on: April 13, 2012, 05:45:49 PM »

Are there any scientific papers out there that use or show different Y DNA STR mutation rates for different haplogroups?
I can not locate one right now but I do recall the hypothesis in at least one paper.   The only one I can show you is that there is a difference between closely related species.

http://www.genetics.org/content/168/1/383.full.pdf+html

chimps vs. people may be too many generations apart, and this study was not Y DNA specific but it does support the concept.   ...
The reason I ask is that is brought up as an objection sometimes, but I've never really seen any strong case to say true mutation rates are different by haplogroups.

When I asked this on Rootsweb or in the past with Vizachero ... BTW Klyosov is a bio-chemist so he should understand...  I consistently get the answer from the scientist/hobbyists that the same mutation rates apply across all haplogroups.  We are all homo sapiens sapiens and are much more alike than different.

I don't know of a study of Y DNA where they use different mutation rates by haplogroup.

It is definitely true that you can observe different mutation rates in different haplogroups but the response to that is ...   it's like flipping a coin, just because it came up heads three times in a row doesn't it will be heads the fourth time. What matters is the expected mutation rate and that doesn't change.
« Last Edit: April 14, 2012, 12:15:37 AM by Mikewww » Logged

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JeanL
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« Reply #30 on: April 13, 2012, 06:27:03 PM »


I've looked at the Busby data in detail and compared it with Marko Heinila's analysis and the study I just cited.

Scientists are not arbitrarily wrong if their budget is limited and they use only 10-15 STRs, but they are dramatically decreasing their precision and dramatically increasing their risk of having a wrong conclusion.

Let's look at one of Busby's illogical application.

"The peopling of Europe and the cautionary tale of Y chromosome lineage R-M269" by Busby et al, 2010.

The 2nd column is the ybp.  I added the "xxx"s to show you which markers Busby used in their R1b-L11/S127 STR diversity calculations.

Quote from: Busby
Fifteen Y-STRs with mutation rates, range of alleles and estimate of duration of linearity. All STRs investigated in this study are shown with their mutation rates (μ), estimated from Ballantyne et al, and range of observed observed alleles, R, with 95% CI is taken from the YHRD. θ(R)/2μ is an estimate of the duration of linearity.
(from Table 1)

Y-STR____ θ(R)/2μ
DYS448___ 25381   
DYS392___ 19244 XXX
DYS438___ 12465 XXX
DYS390___ 9211 XXX
DYS393___ 5648 XXX<<<
DYS439___ 4861 XXX<<<
DYS437___ 4357 XXX<<<
DYS635___ 4221   
DYS456___ 3289   
DYS389II_ 3111 XXX<<<
DYS391___ 2554 XXX<<<
DYS458___ 1944   
DYS19____ 1888 XXX<<<
Y-GATA-H4_ 1630   
DYS389I___ 953 XXX<<< 

Please note that Busby's key conclusion that is a counter-argument to Barlaresque's R1b Neolithic argument is based on the STR diversity of R1b-L11/S127.
Quote from: Busby
(Abstract)
Our analysis reveals no
geographical trends in diversity, in contradiction to expectation under the Neolithic hypothesis...
(Conclusions)
Alternatively,if R-S127 originated prior to the Neolithic wave of expansion, then either it was already present in most of Europe before the expansion, or the mutation occurred in the east, and was spread before or after the expansion, in which case we would expect higher diversity in the east closer to the origins of agriculture, which is not what we observe.

Notice how that the Neolithic revolution started some 10k ybp and was spreading across Europe about 7k ybp.
Quote from: Busby
(Introduction)
Following the development of agriculture in the Fertile Crescent some 10000 years ago, this technology spread from the Near East westward into Europe...

Go back up and look at Busby's Table 1. Only three of the ten STRs they used to draw their conclusion were based on STRs with enough linear duration according to their own evaluation! I put "<<<"'s next to the STRs with linear durity less than 7k ybp.

I've asked this on this forum, on DNA-forums and on Rootsweb. Isn't this a major flaw in their logic? Their own analysis argues against the validity of their primary conclusion, which was to argue against Balaresque.  No one has yet to respond as to the logic.

Their primary conclusion:

Quote from: Busby et al(2011)
We further investigate the young, STR-based time to the most recent common ancestor estimates proposed so far for R-M269-related lineages and find evidence for an appreciable effect of microsatellite choice on age estimates.


It is still well supported by Table-S4 and Figure-4, therefore there isn’t any flaw on their logic pertaining that primary finding. As for them using a mixed set of STRs to counter Balaresque’s argument, well that just goes to show that with the addition of some new populations sampled in this study + the Myres et al. set; the whole East-West quasi-gradient that the Balaresque et al. thought existed disappears. Yes, it is wrong for them to use a mixed set, but what they did was just to show that even under the assumption that STRs linearity does not affect the age estimates there isn’t any perceivable variance distribution in Europe that shows a Neolithic Eastern expansion. Moreover, they even went as far as to use Balaresque’s own set with a different Irish sample and showed that there apparent east-west gradient disappeared, which can be seen on Figure-S2. 
« Last Edit: April 13, 2012, 06:31:08 PM by JeanL » Logged
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« Reply #31 on: April 13, 2012, 06:44:50 PM »

Linear duration of STRs is an issue (I don't deny that,) but you can see that Vizachero considers this to be the issue with haplogroups that are old (of 25k ybp age) and he does not consider R-M269 in that category. 

This is in general agreement with Ken Nordtvedt's simulations although Ken never gives a time break when STR linear duration causes a negative (accuracy risk) return for shorter durations STRs.

So basically because this Vizachero person has a pre-conceived notion that R-M269 has to be less than 25 kbp, then there is no need to worry about loss of linearity on the STRs mutations?  Is this some sort of appeal to authority, because a couple of paragraphs above you mentioned how much you trusted him and all that? This is exactly the same problem I have with Klyosov’s calculation and data, because he thought for some reason that R1b was less than 6000 ybp in Iberia, then he could use whichever STRs he wanted without worrying about loss of linearity, and surprise, surprise, he got a TMRCA that was less than 6000 ybp. As someone who has done quite some good amount of projects and research I can tell you that it is a very rare instance when one gets something so close to what to what one predicts. Not saying that it always has to be the rule, optimally one would get something close to the predictions. But the thing is that when the data is manipulated to yield the desired results then the research losses all its value.  Look, what I’m saying basically, is that maybe R1b-M269 is older than 25 ybp, maybe it isn’t, but assuming that it isn’t is not a well thought motive to not take into account the effects of loss of linearity. Which I assure you, take place in fast mutating STRs way sooner than in a 25 kya period. 
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« Reply #32 on: April 13, 2012, 07:48:44 PM »

It just seems that a person could say that with L21 and its subclades, "Higher Frequency" will equal "Lower Diversity" and that person would be correct.

When I see someone bring up "Diversity" with L21 and/or its Subclades I think, "Why read it?" I know that the place of Highest Frequency has no chance of being the place of Highest Diversity. Which means that in EVERY case the descendants of the first man with a mutated SNP ALWAYS left the area of origin and prospered elsewhere. As a matter of fact, wherever they prospered the most, that place will be the place of Lowest Diversity.

So, when there is one L226 found on the Continent, or even in Britain L226's origin will move out of Ireland because Ireland, as the place of Highest Frequency, cannot be the place of Highest Diversity. I say this with 100% certainty.

It's not so much of an snp leaving and proliferating elsewhere.  Older populations have more time for some lines to go extinct or daughter out, thus leaving more variance/less modality in the case of R1b among the living. All things being equal.
High variance and diversity can correlate with high frequency in places like cities in a relatively recent time frame for reasons outside of genetics.  

As for L21 and really all of L11+, I don't think we can narrow down any particular countries as being the origin anymore.  We will have to see how things shake out with all the new snps.  Then we can revisit the variance of haplotypes.  I think a better approach for a proposed  origin will depend on how the oldest upstream snps cluster.  A couple of years ago France was proposed as an origin for then monolithic L21, but now we have DF21, DF23, and others that are going to be more informative.  The Isles are going to be the origin for some, the continent for others.
« Last Edit: April 13, 2012, 07:51:03 PM by MHammers » Logged

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rms2
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« Reply #33 on: April 13, 2012, 09:21:35 PM »

The Isles will no doubt be the origin point for some subclades of L21 but not for L21 itself (probably not, anyway).

Although it is still possible that L21 could have originated in Ireland (I could be wrong, but I think that is what Miles is hinting at) or somewhere else in the British Isles, that is seeming less and less likely. Look at the recent L21 results among the Basques from the Begoña Martinez-Cruz et al study, for example. It doesn't seem at all likely that that could be the result of Irish input. Likewise, there is too much L21 in France for it to have been the result of Irish input. If one wants to argue for a prehistoric migration from Ireland to the continent, he should have some reason, some evidence, for believing such a thing occurred. Instead, the flow of newcomers, even in prehistoric times, has been into the Isles from the Continent and not really the other way around.

Variance does not absolutely exclude Ireland as the possible place of origin for L21, although Ireland's L21 variance is not the highest in Europe (that honor still belongs to France, I believe). But variance cannot be the sole consideration. There are a number of other factors that, when taken together with variance, militate against Ireland as the birthplace of L21.

« Last Edit: April 13, 2012, 09:26:23 PM by rms2 » Logged

MHammers
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« Reply #34 on: April 13, 2012, 09:40:04 PM »

The Isles will no doubt be the origin point for some subclades of L21 but not for L21 itself (probably not, anyway).

Although it is still possible that L21 could have originated in Ireland (I could be wrong, but I think that is what Miles is hinting at) or somewhere else in the British Isles, that is seeming less and less likely. Look at the recent L21 results among the Basques from the Begoña Martinez-Cruz et al study, for example. It doesn't seem at all likely that that could be the result of Irish input. Likewise, there is too much L21 in France for it to have been the result of Irish input. If one wants to argue for a prehistoric migration from Ireland to the continent, he should have some reason, some evidence, for believing such a thing occurred. Instead, the flow of newcomers, even in prehistoric times, has been into the Isles from the Continent and not really the other way around.

Variance does not absolutely exclude Ireland as the possible place of origin for L21, although Ireland's L21 variance is not the highest in Europe (that honor still belongs to France, I believe). But variance cannot be the sole consideration. There are a number of other factors that, when taken together with variance, militate against Ireland as the birthplace of L21.


Out of 12 L21** members, 2 are Irish, 3 English, 1 Welsh, 1 German, 1 Belarussian, and 4 unknown who might be at least British Isles.  The origin could be British Isles, but not necessarily Ireland.  More testing needed, of course.
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« Reply #35 on: April 13, 2012, 10:02:06 PM »

The Isles will no doubt be the origin point for some subclades of L21 but not for L21 itself (probably not, anyway).

Although it is still possible that L21 could have originated in Ireland (I could be wrong, but I think that is what Miles is hinting at) or somewhere else in the British Isles, that is seeming less and less likely. Look at the recent L21 results among the Basques from the Begoña Martinez-Cruz et al study, for example. It doesn't seem at all likely that that could be the result of Irish input. Likewise, there is too much L21 in France for it to have been the result of Irish input. If one wants to argue for a prehistoric migration from Ireland to the continent, he should have some reason, some evidence, for believing such a thing occurred. Instead, the flow of newcomers, even in prehistoric times, has been into the Isles from the Continent and not really the other way around.

Variance does not absolutely exclude Ireland as the possible place of origin for L21, although Ireland's L21 variance is not the highest in Europe (that honor still belongs to France, I believe). But variance cannot be the sole consideration. There are a number of other factors that, when taken together with variance, militate against Ireland as the birthplace of L21.


Out of 12 L21** members, 2 are Irish, 3 English, 1 Welsh, 1 German, 1 Belarussian, and 4 unknown who might be at least British Isles.  The origin could be British Isles, but not necessarily Ireland.  More testing needed, of course.

It could be, but those totals would seem to indicate the Continent rather than the Isles, given the fact that the British Isles are overwhelmingly better represented in commercial dna testing than anywhere on the Continent.

I think L21 originated on the Continent and got to the Isles as part of the Atlantic Bronze Age trade network, perhaps with Maritime Bell Beaker Folk. My vote goes to somewhere in the vicinity of Morbihan in Bretagne, which was a Maritime Beaker hub.
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eochaidh
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« Reply #36 on: April 13, 2012, 10:21:01 PM »

Rich!!!    We go through this everytime and yet you always persist! I am ABSOLUTELY NOT hinting, implying, stating or otherwise that L21 originated in Ireland! This is YOUR easy way of not addressing the question! The question is about frequency and variance!

Miles Kehoe does NOT believe AND is NOT suggesting that L21 originated in  Ireland!!!! Will you EVER stop Rich? Where could a guy like you go to have this obsession looked at? :) Very, very odd.

AGAIN, doesn't it seem just a wee bit odd to any of you that High Frequency ALWAYS means Low Variance/Diversity. As soon as a High Frequency is found, then HEY! let's look for the smallest frequency, see if it has a High Variance/Diversity, and lo and behold we'll have our origin! As Mike H posted above, this no longer works with all of the subclades, yet there the pattern will persist.

And so, I state with 100% certainty that as soon as L226+ is found outside of Ireland, Ireland will be ruled out as the place of origin! One! One result with a non-Irish name in Britain will do it. Because at that point Ireland will become the one of two places that has the Highest Frequency and therefore it can't possibly have the Highest Variance/Diversity. IT HAS NEVER HAPPENED IN THE HISTORY OF L21 RESEARCH THAT THE HIGEST FREQUENCY HAS EVER BEEN CONSIDERED THE POINT OF ORIGIN ON ANY SNP. Why would L226+ be different?

And, of course, when L226+ is found on the Continent, then the Continent be the origin. If it had EVER happened the other way I wouldn't be posting this. I can feel you people thinking, "Yea, well of course Ireland won't be the origin as soon as one is found outside of Ireland. What's his point?"

I think that High Frequency equals Low Variance/Diversity is fishy. Now, go about twisting my words to say that I am saying that Ireland is the origin of L21. You know no other way.  :)
« Last Edit: April 13, 2012, 10:32:57 PM by eochaidh » Logged

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« Reply #37 on: April 13, 2012, 11:47:38 PM »

Rich!!!    We go through this everytime and yet you always persist! I am ABSOLUTELY NOT hinting, implying, stating or otherwise that L21 originated in Ireland! This is YOUR easy way of not addressing the question! The question is about frequency and variance!

Miles Kehoe does NOT believe AND is NOT suggesting that L21 originated in  Ireland!!!! Will you EVER stop Rich? Where could a guy like you go to have this obsession looked at? :) Very, very odd.

AGAIN, doesn't it seem just a wee bit odd to any of you that High Frequency ALWAYS means Low Variance/Diversity. As soon as a High Frequency is found, then HEY! let's look for the smallest frequency, see if it has a High Variance/Diversity, and lo and behold we'll have our origin! As Mike H posted above, this no longer works with all of the subclades, yet there the pattern will persist.

And so, I state with 100% certainty that as soon as L226+ is found outside of Ireland, Ireland will be ruled out as the place of origin! One! One result with a non-Irish name in Britain will do it. Because at that point Ireland will become the one of two places that has the Highest Frequency and therefore it can't possibly have the Highest Variance/Diversity. IT HAS NEVER HAPPENED IN THE HISTORY OF L21 RESEARCH THAT THE HIGEST FREQUENCY HAS EVER BEEN CONSIDERED THE POINT OF ORIGIN ON ANY SNP. Why would L226+ be different?

And, of course, when L226+ is found on the Continent, then the Continent be the origin. If it had EVER happened the other way I wouldn't be posting this. I can feel you people thinking, "Yea, well of course Ireland won't be the origin as soon as one is found outside of Ireland. What's his point?"

I think that High Frequency equals Low Variance/Diversity is fishy. Now, go about twisting my words to say that I am saying that Ireland is the origin of L21. You know no other way.  :)

Miles,

As the number of haplotypes increases in a population there tends to be a saturation towards a modal haplotype which causes the low variance.  The behavior of str's and their relationship with snp's is uncertain.  The trail of L21 will unlikely be solved by variance anyway.  Most of them (snp's) seem to cluster by origin in less than a millenium's time frame.  Basically rapid expansion via maritime networks, possibly in the bronze age. 

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eochaidh
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« Reply #38 on: April 14, 2012, 12:13:32 AM »

Mike H,

     And, of course, the descendants of the first boy born with the mutated SNP could have stayed in the origin for one generation or 10. With the chance that a brother(s) or cousin(s) could have migrated alone or with male relations at anytime between or after. Some may have prospered, some may have died out. Somehow the logic of multiple possibilities seems to be missing when it all comes down to Frequency and Variance/Diversity.

     Luckily for all of us the onslaught of new SNPs has begun to cause some entrenched thinking to wobble.
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« Reply #39 on: April 14, 2012, 12:28:40 AM »

Mike H,

     And, of course, the descendants of the first boy born with the mutated SNP could have stayed in the origin for one generation or 10. With the chance that a brother(s) or cousin(s) could have migrated alone or with male relations at anytime between or after. Some may have prospered, some may have died out. Somehow the logic of multiple possibilities seems to be missing when it all comes down to Frequency and Variance/Diversity.

     Luckily for all of us the onslaught of new SNPs has begun to cause some entrenched thinking to wobble.

The logic is sound.  It's only a rule of thumb, there will always be exceptions.
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« Reply #40 on: April 14, 2012, 01:05:19 AM »

I think "rules of thumb" too easily become entrenched thinking.

When L21+ was first discovered we were still under an archaeological spell; if there wasn't a pot or ornament to connect two groups, then it didn't happen. Since then we have grown to embrace a vibrant Atlantic coast. Many of us were laughed at when we brought up the idea of such a thing.

Still, as many people embrace this vibrant, seafaring, Atlantic Coast, many are unable to picture a group of people leaving Ireland on a boat. As I've said before, Ireland is the Black Hole of genetics; what goes in never comes out. Once in Ireland, the seafarer loses all vibrancy, he and his descendants will never leave. Atlantic Bronze age travel means migtation to and from all coastal and island countries other than Ireland. Ireland is a one way street. That is why I say wirh 100% certainty that L226+ will lose any chance of having Ireland as its origin as soon as one result is found outside of Ireland.
« Last Edit: April 14, 2012, 01:06:20 AM by eochaidh » Logged

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« Reply #41 on: April 14, 2012, 02:49:38 AM »

I created a strawman which attempts to explain the Atlantic route. Morbihan in France would appear to be a central hub in the four ages Atlantic, Megalithic, Copper, Bronze and Iron.
Prior to arriving at Morbihan, IMO, L21 or it's ancestor came from Tartessos in Iberia and Galecia where there is strong evidence of Celtic language and culture development.
Of course there is an equally strong Rivers route which also includes U106 and U152. I believe the use of river and maritime routes was a matter of routine and bidirectional and accomplished in months rather than a Demic diffusion type wave taking centuries. The Demic diffusion did happen but they were following in the footsteps of those who went before and spreading inland away from coasts and rivers.. I don't believe that L21 marched across the continent like Lemmings and walked over the cliffs at Dun Aengus or were sucked into a black hole. There were many back migrations and onward migrations which cannot be explained by STR diversity, eg L21 or U106 in the US.
 
As always I am wary of the age estimates but it is the best we have to go with at the moment.
The STR clock is broken but even a broken clock tells the right time twice a day.
We depend on STR analysis and new SNPs but ultimately the granualarity and certainty will be provided by new SNP discovery and the holy grail is full Y sequencing. We also need new methodologies and tools such as matching halpogroup analysis, both Y and mtDNA to match the DNA to localities and tribal affiliations.
The "People of the British Isles" and "Irish DNA Atlas" project and good old fashioned genealogy should help in this regard.
We have under estimated the role of mtDNA, although it is half the population and recent analysis would point to similar migration routes. We also have a lot to learn from aDNA both Y and mtDNA.
Above all we need a large amount of common sense and patience. The tools will come and full sequencing will arrive. We can barely keep up with the flood of new SNPs as it stands.

http://m.box.com/view_shared/d0nr7768zv18ht6tk28i

https://www.box.net/shared/pf653l1r181ry7r61ix4
« Last Edit: April 14, 2012, 03:49:33 AM by Heber » Logged

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R1b1a2a1a1b4  L459+ L21+ DF21+ DF13+ U198- U106- P66- P314.2- M37- M222- L96- L513- L48- L44- L4- L226- L2- L196- L195- L193- L192.1- L176.2- L165- L159.2- L148- L144- L130- L1-
Paternal L21* DF21


Maternal H1C1



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« Reply #42 on: April 14, 2012, 07:16:03 AM »

Rich!!!    We go through this everytime and yet you always persist! I am ABSOLUTELY NOT hinting, implying, stating or otherwise that L21 originated in Ireland! This is YOUR easy way of not addressing the question! The question is about frequency and variance!

Miles Kehoe does NOT believe AND is NOT suggesting that L21 originated in  Ireland!!!! Will you EVER stop Rich? Where could a guy like you go to have this obsession looked at? :) Very, very odd.

AGAIN, doesn't it seem just a wee bit odd to any of you that High Frequency ALWAYS means Low Variance/Diversity. As soon as a High Frequency is found, then HEY! let's look for the smallest frequency, see if it has a High Variance/Diversity, and lo and behold we'll have our origin! As Mike H posted above, this no longer works with all of the subclades, yet there the pattern will persist.

And so, I state with 100% certainty that as soon as L226+ is found outside of Ireland, Ireland will be ruled out as the place of origin! One! One result with a non-Irish name in Britain will do it. Because at that point Ireland will become the one of two places that has the Highest Frequency and therefore it can't possibly have the Highest Variance/Diversity. IT HAS NEVER HAPPENED IN THE HISTORY OF L21 RESEARCH THAT THE HIGEST FREQUENCY HAS EVER BEEN CONSIDERED THE POINT OF ORIGIN ON ANY SNP. Why would L226+ be different?

And, of course, when L226+ is found on the Continent, then the Continent be the origin. If it had EVER happened the other way I wouldn't be posting this. I can feel you people thinking, "Yea, well of course Ireland won't be the origin as soon as one is found outside of Ireland. What's his point?"

I think that High Frequency equals Low Variance/Diversity is fishy. Now, go about twisting my words to say that I am saying that Ireland is the origin of L21. You know no other way.  :)

Lol.

Now, golly, why would I ever think that you were once again (for the umpteenth time) pushing the overweening Irish nationalist schtick?

It gets old, Miles.
« Last Edit: April 14, 2012, 07:16:35 AM by rms2 » Logged

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« Reply #43 on: April 14, 2012, 07:26:28 AM »

You should probably read the two studies on "Surfing the Wave". I think Klopfstein was the primary author.  I've pointed to them before.  No one is saying that concept always applies, just that it may apply in some situations.

Would L459 & Z245 cause problems for "Surfing the Wave" with respects to L21 ?

It's looking increasingly unlikely that an L21+ L459- and/or Z245- person is going to turn up (or L21- L459+ and/or Z245+) and even if such a person were found they probably wouldn’t have much company.

How likely is it that all three of these SNPs formed at the front of a population expansion without splitting up, and then there is also Z260 & Z290 to think about which will probably cover at the least a fairly large proportion of L21+ folk.
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« Reply #44 on: April 14, 2012, 11:26:09 AM »

.. As the number of haplotypes increases in a population there tends to be a saturation towards a modal haplotype which causes the low variance.  The behavior of str's and their relationship with snp's is uncertain.  The trail of L21 will unlikely be solved by variance anyway. 

Agreed, Skip M was trying to make the same point on the need for true scientifically designed random sampling.

The trail of SNPs in the phylogeny of L21 or any clade is critical, and I agree, is more important that STR variance.   STR variance is just another data point to be used in conjunction with the phylogeny (which is what interclade calculations support), the archaeology, etc.
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« Reply #45 on: April 14, 2012, 11:29:17 AM »

You should probably read the two studies on "Surfing the Wave". I think Klopfstein was the primary author.  I've pointed to them before.  No one is saying that concept always applies, just that it may apply in some situations.

Would L459 & Z245 cause problems for "Surfing the Wave" with respects to L21 ?

It's looking increasingly unlikely that an L21+ L459- and/or Z245- person is going to turn up (or L21- L459+ and/or Z245+) and even if such a person were found they probably wouldn’t have much company.

How likely is it that all three of these SNPs formed at the front of a population expansion without splitting up, and then there is also Z260 & Z290 to think about which will probably cover at the least a fairly large proportion of L21+ folk.
I don't know, but I don't think your argument changes much.

How often do SNPs occur?  Isn't it something like one per generation?   I've heard statements like that.  If it is some frequency like that, having 3 SNPs in 3 generations that align is not a big deal.

The issue is just finding all of those SNPs, or at least the ones that don't go extinct. Probably more L21 people have been through full genome or WTY testing than any other subclade. We shouldn't look at SNPs as all that rare. This is their great promise for the future.
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« Reply #46 on: April 14, 2012, 12:23:30 PM »

Linear duration of STRs is an issue (I don't deny that,) but you can see that Vizachero considers this to be the issue with haplogroups that are old (of 25k ybp age) and he does not consider R-M269 in that category.  

This is in general agreement with Ken Nordtvedt's simulations although Ken never gives a time break when STR linear duration causes a negative (accuracy risk) return for shorter durations STRs.

So basically because this Vizachero person has a pre-conceived notion that R-M269 has to be less than 25 kbp, then there is no need to worry about loss of linearity on the STRs mutations?  Is this some sort of appeal to authority, because a couple of paragraphs above you mentioned how much you trusted him and all that? ....

JeanL, I'm not really hoping to change your mind so I wasn't really thinking of invoking Vincent Vizachero's name as an appeal to authority although I guess you could consider it that. My intent is really just to let the undecided read along and make up their own minds. I am not the statistician to argue this stuff in-depth so I wanted to refer to who I find credible.

At one time time I believed R1b was Cro-Magnon in Europe and was up to 35k ybp old. I was influenced by National Genographic's Spencer Wells. However, people like Vizachero, Chandler, Nordtvedt, Vernande and Stevens convinced me, really not by their authority (Spencer Wells as more authority in this field) but by logic and data. I'm just telling you where I'm getting my thinking from. Chandler is the "rates" guy and Nordtvedt is the "TMRCA" guy in this field as far as hobbyists go, and it is my opinion they out think the actual academic folks on these issues. No doubt about it, Nordtvedt has provided several innovations to TMRCA calculation methods. I think I should add Marko Heinila as well, but there are others. People like Sandy Patterson can create their own statistical simulations and try out different approaches.

I have changed my mind in the past and I'm sure I will in the future so I'm open if you can present a logical case. Most people seem to just throw out objections, but don't really provide a full counter-proposal.  I think the Busby paper is an example.

This is exactly the same problem I have with Klyosov’s calculation and data, because he thought for some reason that R1b was less than 6000 ybp in Iberia, then he could use whichever STRs he wanted without worrying about loss of linearity, and surprise, surprise, he got a TMRCA that was less than 6000 ybp. ....

Like it or not, hobbyists who invested the most time and discussion (and I think are most credible) on TMRCAs and STR diversity - Ken, Marko, Anatole (Klyosov), Tim Janzen, Vince, etc. all come out with R-M269 being fairly young, like the 4-8k ybp age.  The Chief Scientist at FTDNA, Michael Hammer, says R-M269 is "4-8k years" old.

Klyosov's method is different than Nordtvedt as is Heinila's.  Still their results are similar.  They do explain their methods and they are available.
« Last Edit: April 14, 2012, 12:41:09 PM by Mikewww » Logged

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« Reply #47 on: April 14, 2012, 12:47:41 PM »

You should probably read the two studies on "Surfing the Wave". I think Klopfstein was the primary author.  I've pointed to them before.  No one is saying that concept always applies, just that it may apply in some situations.

Would L459 & Z245 cause problems for "Surfing the Wave" with respects to L21 ?

It's looking increasingly unlikely that an L21+ L459- and/or Z245- person is going to turn up (or L21- L459+ and/or Z245+) and even if such a person were found they probably wouldn’t have much company.

How likely is it that all three of these SNPs formed at the front of a population expansion without splitting up, and then there is also Z260 & Z290 to think about which will probably cover at the least a fairly large proportion of L21+ folk.
I don't know, but I don't think your argument changes much.

How often do SNPs occur?  Isn't it something like one per generation?   I've heard statements like that.  If it is some frequency like that, having 3 SNPs in 3 generations that align is not a big deal.

The issue is just finding all of those SNPs, or at least the ones that don't go extinct. We shouldn't look at SNPs as all that rare.

Ken quoted an estimated figure of 1 SNP per generation on average but I was told this would work out as 1/2 because only 1/2 the Y chromosome is readable or something, got to be honest I got lost in the conversation at that point :)

however as you pointed out most male lines die out, which is presumably what happened to L21-,L459+ or  L21+,Z245- (and any of the other possible combinations), but I thought reduced extinction rates was one of the facets of the wave surfing idea ?

At the end of the day probably the biggest limiting factor isn't the rarity of SNPs but the difficulty in identifying them.

This brings me back round to the point that 5 SNPs (L21 included) were found at the root of L21 in the 1000 genome project but only one for U106, P312 & U152 as far as I can remember.

Of course this could just be down to happenstance but to my mind there is also a reasonable possibility that this is relevant to the history of L21.
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« Reply #48 on: April 14, 2012, 12:50:24 PM »

The STR clock is broken but even a broken clock tells the right time twice a day.

I wouldn't use the word broken nor treat this is as a singular clock.  There are 67 (up to 111) STR clocks now widely available.  Some may actually be practically broken for long time periods.  Some STRs probably work better than others, but the problem is we don't truly know which is which.  This is where the power of statistics and law of large numbers is of immense help, to blend the all of the clocks together as is appropriate.

ultimately the granualarity and certainty will be provided by new SNP discovery and the holy grail is full Y sequencing.

I agree although I wouldn't use the same terminology. The greater benefits are realized when the SNP phylogeny AND STR diversity are considered in conjunction with each other.
« Last Edit: April 14, 2012, 12:51:01 PM by Mikewww » Logged

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« Reply #49 on: April 14, 2012, 12:56:09 PM »

You should probably read the two studies on "Surfing the Wave". I think Klopfstein was the primary author.  I've pointed to them before.  No one is saying that concept always applies, just that it may apply in some situations.

Would L459 & Z245 cause problems for "Surfing the Wave" with respects to L21 ?

It's looking increasingly unlikely that an L21+ L459- and/or Z245- person is going to turn up (or L21- L459+ and/or Z245+) and even if such a person were found they probably wouldn’t have much company.

How likely is it that all three of these SNPs formed at the front of a population expansion without splitting up, and then there is also Z260 & Z290 to think about which will probably cover at the least a fairly large proportion of L21+ folk.
I don't know, but I don't think your argument changes much.

How often do SNPs occur?  Isn't it something like one per generation?   I've heard statements like that.  If it is some frequency like that, having 3 SNPs in 3 generations that align is not a big deal.

The issue is just finding all of those SNPs, or at least the ones that don't go extinct. We shouldn't look at SNPs as all that rare.

Ken quoted an estimated figure of 1 SNP per generation on average but I was told this would work out as 1/2 because only 1/2 the Y chromosome is readable or something, got to be honest I got lost in the conversation at that point :)
Believe me, I get lost plenty.

If only 1/2 an SNP occurs per generation, then it would take only 6 generations to get 3, but these are just averages anyway.

however as you pointed out most male lines die out, which is presumably what happened to L21-,L459+ or  L21+,Z245- (and any of the other possible combinations), but I thought reduced extinction rates was one of the facets of the wave surfing idea ?

We don't know if L459 or Z245 is upstream of L21 or not.  Unfortunately, NOT many P312* folks have tested for those.

.. but you just said it, most lineages die out.  Everyone on the wave of an expansion does not prosper. As far as paternal lineages, it looks like those who prosper are fairly limited in number, it's just they do a ton of damage (so to speak.)
« Last Edit: April 14, 2012, 01:03:18 PM by Mikewww » Logged

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