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Maliclavelli
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« Reply #125 on: May 16, 2012, 11:13:39 AM »

This to say what? That probably Iberia (and Basques) aren’t at the origin of L23, L150, L51 and so on. If you note, the presence in Iberia of L51 in the RRocca’s map, as I have already said, is in places colonized by Italian agriculturalists by sea 7500YBP. I know that they believe that hg. R is younger, but you should know too that I don’t agree with them.
These haplotypes aren’t Basque, I think (and the autosmal isn’t a proof, because if a Y entered the Basque pool 2000YBP, you don’t find now anything of it at autosomal level), also because these are two very different haplotypes and Basques haven’t anything of intermediate. To pass from DYS389=13-29 (or +16) to 12-28 or to 13-30, it needs much time, many thousands of years, and the people of origin should have much more of the modal, what Basques don’t get. A similar demonstration I gave for Basque R-M269*, I think having demonstrated not Basque in its origin.

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JeanL
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« Reply #126 on: May 16, 2012, 11:36:36 AM »

These haplotypes aren’t Basque, I think (and the autosmal isn’t a proof, because if a Y entered the Basque pool 2000YBP, you don’t find now anything of it at autosomal level), also because these are two very different haplotypes and Basques haven’t anything of intermediate. To pass from DYS389=13-29 (or +16) to 12-28 or to 13-30, it needs much time, many thousands of years, and the people of origin should have much more of the modal, what Basques don’t get. A similar demonstration I gave for Basque R-M269*, I think having demonstrated not Basque in its origin.



Well to say that those two haplotypes aren’t Basque is simply wishful thinking. I already laid out my reasoning. But, if you think that an intrusion from elsewhere(i.e. Jewish, Eastern Europe, even Italy) dating back to the historical era(i.e. 0-2000 ybp) leaves no trace autosomally, then you might as well accept that R1b could indeed have originated in West Asia(4000-8000 ybp), became the majority haplogroup in Basques, and left no Autosomal trace.  I never said that these L23+(xL51) haplotypes originated in situ, I said that there is no proof that they came in the historical era. Moreover, this is a random sample of 6, why would one expect to find anything intermediate if the sample size is so small. Also, the people where a SNP originates do not necessarily have to have more of the modal, quite contrary, there is more time there for the haplotypes to mutate, ergo the will be less modal haplotypes relative to the whole pool and in places where it arrived later.

PS: The haplotypes differ from one another by 6 mutations.   

HGDP00511 BAS M269 14 12 16 24 11 13 12 15 12 13 19 15 16 23 11     
HGDP00515 BAS M269 14 13 17 25 11 13 12 15 12 12 19 15 16 23 13 

All this means, is that they are really ancient in the region, they are probably survivors of the R-L51, and R-P312 expansions, and that is why they are so vastly different from one another.
« Last Edit: May 16, 2012, 11:44:42 AM by JeanL » Logged
Maliclavelli
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« Reply #127 on: May 16, 2012, 12:02:13 PM »

Yes, of course we need more data and everything is possible. I think that the place of origin of a haplogroup is that where there is a path of that haplogroup, and it seems to me that Basques or Iberia haven’t it, but everything is still possible till we haven’t much more data.
Many years ago I said to Sam Vass that their haplotypes were of Iberian origin and I discovered on SMGF a Basque (probably) R1b1* I put on ySearch: Arellano.
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Maliclavelli


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alan trowel hands.
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« Reply #128 on: May 16, 2012, 12:45:27 PM »

One of the significance of the L51* distribution compared to beakers is as I have said they dont include the later beaker areas such as northern Europe, the isles (apart from the one blob in southern Ulster).  It could all be chance but I doubt it.  It suggests that the initial period of beaker spread included L51* but the secondary phase didnt.  So that would all but rule out a northern European entry of L51* and as the map implies it must have entered from the west Med. by sea or perhaps along the Alpine fringe.  It certainly wouldnt support a movement any further north than the Alps.  That of course is not exactly stunning as it is pretty in line with Muller and Willigen's dates.  It seems to tie their basic model (maybe not every detail) in extremely well with L51*.  Now I understand that L51* variance also ties in extremely well with it being part of the very early phase of beaker culture c. 2800-2600BC or something like that. 

The question it raised to me is where in this ealry beaker block the minority of L11* that was ancestral to L11* was located.  It was after all one L51* man who developed the L11* SNP.  I would tend to think that L51* was from the start of the beaker spread a minority within an L11* (probably P312 giving way to its major subclades) group because the same areas came to be predominantly L11 and derived but its a handy proxy for the early movements of L11 and probably P312 too. 

If L51* is a proxy for  ifor early L11*/P312 movements then it narrows down the areas in which P312 could have occurred to that L51* zone. 

Although its a leap of faith you could say that this early movement exploring happened just before U152 and L21 SNPs had occurred given the lack of U152 in Atlantic Iberia and L21 in some of the other areas in the L51* distribution.  They likely occurred locally just after this movement that has been snapshoted by the L51* element. 

So, the early period proxied by the L51* minority cousins within it perhaps occurred at the point when DF 27 had occurred but immediately before U152 and L21. So, I woud guess we are looking at an L51*, L11*, P312* and DF 27 phase.  That might actually fit the variance rather well if we are looking at a point around 2600BC or just before. 

I have a hunch that the isolated L51* pocket in central Europe could be an echo of an L51* and L11* movement in that direction, perhaps is represented by the people in the recent beaker burial found to ne M268xU106.  I dont think U106 occurred until later when some of the L11* folks had reached Poland.  The core in SE France could have around the same time but fractionally behind developed locally U152 just before it spread into Italy.  The branch of L51* heading towards NW France could likely have been among a group of P312* giving birth to L21* while the L51* heading west (apparently by a marine leap) could have been a minor element in a DF 27 dominated  movement.       

 
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razyn
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« Reply #129 on: May 16, 2012, 03:28:06 PM »

If L51* is a proxy for early L11*/P312 movements then it narrows down the areas in which P312 could have occurred to that L51* zone.

Yes, but if it isn't (a proxy, &c.), it doesn't.  I keep wondering whether L51* is a proxy for low resolution testing, several years ago -- and whether that's what Rich R has mapped.  I'm not persuaded that today's paragroup (L51*, or others) points to much more than tomorrow's SNP discoveries. And if that fear turns out to be grounded, the point along young L11's itinerary at which P312 really did occur might be somewhere not highlighted on the said map.  Anyway, we shall see.

Quote
as the map implies it must have entered from the west Med. by sea or perhaps along the Alpine fringe.  It certainly wouldn't support a movement any further north than the Alps.

Well, probably not a land movement, of a migrating population, north of the Alps.  And that's if the map is right... or, rather, a map of what you think it is.  Again, we shall see.

I agree with most of what you said here, except for having reservations about one or two of its premises.  I don't mean to be a pest, but also don't want to slam any doors yet on alternate lines of investigation.
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Mark Jost
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« Reply #130 on: May 16, 2012, 11:41:21 PM »


For what its worth, about eight months ago I utilized the Busby 15-Str study data and ran some Phylograms and a Fluxus to see how the branching fell out. If anyone is interested. The Goggle stored Zip file contains Spreadsheets and PDFs.

https://docs.google.com/open?id=0By9Y3jb2fORNYjdYcW54ODA4RFk

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)
alan trowel hands.
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« Reply #131 on: May 17, 2012, 07:43:54 AM »

If L51* is a proxy for early L11*/P312 movements then it narrows down the areas in which P312 could have occurred to that L51* zone.

Yes, but if it isn't (a proxy, &c.), it doesn't.  I keep wondering whether L51* is a proxy for low resolution testing, several years ago -- and whether that's what Rich R has mapped.  I'm not persuaded that today's paragroup (L51*, or others) points to much more than tomorrow's SNP discoveries. And if that fear turns out to be grounded, the point along young L11's itinerary at which P312 really did occur might be somewhere not highlighted on the said map.  Anyway, we shall see.

Quote
as the map implies it must have entered from the west Med. by sea or perhaps along the Alpine fringe.  It certainly wouldn't support a movement any further north than the Alps.

Well, probably not a land movement, of a migrating population, north of the Alps.  And that's if the map is right... or, rather, a map of what you think it is.  Again, we shall see.

I agree with most of what you said here, except for having reservations about one or two of its premises.  I don't mean to be a pest, but also don't want to slam any doors yet on alternate lines of investigation.

Even if its not a proxy the L51* group seems to have followed the pre-2600 beaker networks judging by distribution.  An alternative to it being a small element travelling with L11 groups is that it is the signiture of an early exploratory phase (maybe something like the tail end of Jean's Stelae People) where the beaker networks were judt developing and people were exploring and moving along what would later be thought of as the beaker network.  Of course that would have to mean that a cousinly group of L11 folks then followed behing the exact same networks and everywhere they went the L11 people swamped the L51* lines.  That is not impossible but it seems very unlikely given that it would require that in all the far flung corners of the beaker world L11 just so happened to always outdo L51* lines time and time again.  

More likely IMO that the initial beaker groups featured only a little L51* and L11* and a lot more P312 and its very earliest subclades.  The non-appearance of L51* in the beaker areas settled after 2600BC could simply be down to loss of a small minority lineage during a process of constant fission of the group.

  
« Last Edit: May 17, 2012, 07:48:25 AM by alan trowel hands. » Logged
alan trowel hands.
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« Reply #132 on: May 17, 2012, 09:29:55 AM »

I also found this map on Rokus's blog.  Its the variance of L23* from Myres sample.

http://rokus01.files.wordpress.com/2010/09/l23.png

It again in terms of Europe west of the Adriatic bears a strong resemblance to Willigen and Mullers beaker dating (in relative terms, I am ignorng the actual dates). OK its not as eligance map as that that RR created for the distribution of L51* but it does bear a strong resemblance to the general sequence of the spread of beaker. So again I would hypothesis that a very small L23* element travelled with the L51* group into the west.  So, this L23* group could be a proxy for the beaker and pre-beaker group that first brought R1b into western Europe.  The route into western Europe does again look to have been a southern one or at a stretch an Alpine one.   What is interesing about the L23* map is that unlike L51* it is not restricted to the beaker network and includes a huge swathe to the east.  The map is probably as close as we get to understanding the direction and origin of L23 in pre-beaker times.  Unfortunately its a rather huge area.
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alan trowel hands.
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« Reply #133 on: May 17, 2012, 09:52:06 AM »

Actually that map and its relative ages of various areas looks rather like L23 was born in northern Mesolopamia in the Neolithic and spread from there into both sides of the Black Sea.  That would have put L23* is the steppes, Romania and Anatolia during the PIE formation period.  In the mix as it were in all the locations that have been suggested for PIE. 

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alan trowel hands.
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« Reply #134 on: May 17, 2012, 10:09:32 AM »

and a futher thought is if L23* moved out of northern Mesopotamia and was already in the steppes, Anatolia and the Balkans in three seperated groups in say 4000BC then that also bears a bit of a parallel to the PIE/Anatolian split.

Anyway before getting too complicated, I would ask for opinions on this - if L23" was one of the groups (presimably a dairy element infiltratng) in the steppes say 4000BC and they were among R1a hunters morphing inot nomadic pastoralists then who is to say which one of the two groups actually spoke IE first?  Perhaps the north Mesopotamian L23 pushed into Anatolia (and maybe also crossing the Bosphorus) in one branch and another headed through the Caucuses into the steppes. That sort of scenario does bear some resemblence to the linguistic one where the Anatolian branch split off early from the group who were to become PIE.   I am not saying that happened but I cant see any reasson why it is not an option. 
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Mark Jost
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« Reply #135 on: May 17, 2012, 12:41:04 PM »


For what its worth, about eight months ago I utilized the Busby 15-Str study data and ran some Phylograms and a Fluxus to see how the branching fell out. If anyone is interested. The Goggle stored Zip file contains Spreadsheets and PDFs.

https://docs.google.com/open?id=0By9Y3jb2fORNYjdYcW54ODA4RFk

MJost
(2nd version post. Deleted my first due to incorrect STR column alignment in Ken's Gen sheet.)

Using Modified KenN Gen111T using Busby 15 marker study which the Gen sheet can use only 13 Markers.

Result:

M269 and S116(P312)

YrsPerGen*   Count   AGE   Generations   YBP   Founder   Generations   YBP      
25   N=177    M269 GA coal=   182.6   4,565.9   GA=   202.9   5,071.4      
                           
25   N=717   S116/P312 GB coal=   130.5   3,261.4   GB=   148.4   3,710.2      
                           
TMRCA      Founder                     
25      GAB=   195.7   4,892.5            


M269 and S21(U106)

YrsPerGen*   Count   AGE   Generations   YBP   Founder   Generations   YBP      
25   N=177    M269 GA coal=   182.6   4,565.9   GA=   202.9   5,071.4      
                           
25   N=141   S21/U106 GB coal=   139.0   3,474.7   GB=   153.1   3,827.6      
                           
TMRCA      Founder                     
25      GAB=   193.5   4,837.4            


M269 and L21
 
YrsPerGen*   Count   AGE   Generations   YBP   Founder   Generations   YBP      
25   N=177    M269 GA coal=   182.6   4,565.9   GA=   202.9   5,071.4      
                           
25   N=648   L21 GB coal=   119.5   2,988.6   GB=   130.0   3,249.8      
                           
TMRCA      Founder                     
25      GAB=   224.4   5,609.4            
   
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)
JeanL
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« Reply #136 on: May 17, 2012, 01:15:47 PM »

and a futher thought is if L23* moved out of northern Mesopotamia and was already in the steppes, Anatolia and the Balkans in three seperated groups in say 4000BC then that also bears a bit of a parallel to the PIE/Anatolian split.

Anyway before getting too complicated, I would ask for opinions on this - if L23" was one of the groups (presimably a dairy element infiltratng) in the steppes say 4000BC and they were among R1a hunters morphing inot nomadic pastoralists then who is to say which one of the two groups actually spoke IE first?  Perhaps the north Mesopotamian L23 pushed into Anatolia (and maybe also crossing the Bosphorus) in one branch and another headed through the Caucuses into the steppes. That sort of scenario does bear some resemblence to the linguistic one where the Anatolian branch split off early from the group who were to become PIE.   I am not saying that happened but I cant see any reasson why it is not an option. 

I just want to add a couple of thoughts to it:

1-This is a paragroup, which is L23(xM412/L51), I too did the calculations of variance for the paragroup L23*, and found it to be the oldest at the Caucasus, however, this was only observed when all Caucasian populations were sampled as a whole, individually, the variance decayed greatly.  You can find more about it here: http://i1133.photobucket.com/albums/m582/jeanlohizun/Myresetal2010Herreraetal2010L23xL51data.jpg

2-The graph you provided shows Isoclines based on the data collected from Table-S2, more specifically it shows the Coalescent times rather than the variance. Myres et al(2010) used the evolutionary rate to calculate those coalescence times. The main problem here, is that the data for L23* is as follows:

Greece(n=15) TD=6763 ybp
Slovakia(n=10) TD=5153 ybp
Switzerland(n=10) TD=7246 ybp
Hungary(n=7) TD=5952 ybp
Romania(n=12) TD=11199 ybp
Caucasus(n=32) TD=12217 ybp
Bashkirs(n=29) TD=1624 ybp
Pakistan(n=5) TD=14493
Turkey(n=58) TD=11057 ybp
Italy(n=14) TD=9526 ybp
Poland(n=7) TD=3106 ybp

Those dates were used to construct the map you provided:

http://rokus01.files.wordpress.com/2010/09/l23.png

As you can see the reason why it appears as if Northern Iran, Afghanistan and Pakistan have such an old date, is due to the anomalous results from Pakistan, which are likely due to the small sample size. However given that we have no data from Iran, at least not from Myres et al(2010), it is really hard to come to any reasonable conclusion that L23 originated in Northern Mesopotamia. Something else to look at, is that the TD of Romania, and of Turkey are very similar, and this is something I observed in my own calculations of Variance for L23(xL51). However, my results differ from theirs, in that I calculate the modal in a locus basis, whereas they do it finding the median haplotype per population.  If I was forced to postulate a hypothesis based on the data published by Myres et al(2010); I would say that given the relatively significant presence of R1b-M269(xL23) in the Balkans, and the relatively significant variance of R1b-L23(xL51) in Romania, that L23 was born somewhere near Romania either to the West of it, or to the East of it.

« Last Edit: May 17, 2012, 01:19:57 PM by JeanL » Logged
JeanL
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« Reply #137 on: May 17, 2012, 01:18:54 PM »

(2nd version post. Deleted my first due to incorrect STR column alignment in Ken's Gen sheet.)

Using Modified KenN Gen111T using Busby 15 marker study which the Gen sheet can use only 13 Markers.

Result:

M269 and S116(P312)

YrsPerGen*   Count   AGE   Generations   YBP   Founder   Generations   YBP      
25   N=177    M269 GA coal=   182.6   4,565.9   GA=   202.9   5,071.4      
                           
25   N=717   S116/P312 GB coal=   130.5   3,261.4   GB=   148.4   3,710.2      
                           
TMRCA      Founder                     
25      GAB=   195.7   4,892.5            


M269 and S21(U106)

YrsPerGen*   Count   AGE   Generations   YBP   Founder   Generations   YBP      
25   N=177    M269 GA coal=   182.6   4,565.9   GA=   202.9   5,071.4      
                           
25   N=141   S21/U106 GB coal=   139.0   3,474.7   GB=   153.1   3,827.6      
                           
TMRCA      Founder                     
25      GAB=   193.5   4,837.4            


M269 and L21
 
YrsPerGen*   Count   AGE   Generations   YBP   Founder   Generations   YBP      
25   N=177    M269 GA coal=   182.6   4,565.9   GA=   202.9   5,071.4      
                           
25   N=648   L21 GB coal=   119.5   2,988.6   GB=   130.0   3,249.8      
                           
TMRCA      Founder                     
25      GAB=   224.4   5,609.4            
   
MJost

Would you mind doing the same calculations in all the P15+(G2a+) haplotypes found in the latest study published about Haplogroup G.

The haplotypes are found on Supplementary Table-3.

http://www.nature.com/ejhg/journal/vaop/ncurrent/suppinfo/ejhg201286s1.html
« Last Edit: May 17, 2012, 01:20:34 PM by JeanL » Logged
alan trowel hands.
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« Reply #138 on: May 17, 2012, 02:31:14 PM »

and a futher thought is if L23* moved out of northern Mesopotamia and was already in the steppes, Anatolia and the Balkans in three seperated groups in say 4000BC then that also bears a bit of a parallel to the PIE/Anatolian split.

Anyway before getting too complicated, I would ask for opinions on this - if L23" was one of the groups (presimably a dairy element infiltratng) in the steppes say 4000BC and they were among R1a hunters morphing inot nomadic pastoralists then who is to say which one of the two groups actually spoke IE first?  Perhaps the north Mesopotamian L23 pushed into Anatolia (and maybe also crossing the Bosphorus) in one branch and another headed through the Caucuses into the steppes. That sort of scenario does bear some resemblence to the linguistic one where the Anatolian branch split off early from the group who were to become PIE.   I am not saying that happened but I cant see any reasson why it is not an option. 

I just want to add a couple of thoughts to it:

1-This is a paragroup, which is L23(xM412/L51), I too did the calculations of variance for the paragroup L23*, and found it to be the oldest at the Caucasus, however, this was only observed when all Caucasian populations were sampled as a whole, individually, the variance decayed greatly.  You can find more about it here: http://i1133.photobucket.com/albums/m582/jeanlohizun/Myresetal2010Herreraetal2010L23xL51data.jpg

2-The graph you provided shows Isoclines based on the data collected from Table-S2, more specifically it shows the Coalescent times rather than the variance. Myres et al(2010) used the evolutionary rate to calculate those coalescence times. The main problem here, is that the data for L23* is as follows:

Greece(n=15) TD=6763 ybp
Slovakia(n=10) TD=5153 ybp
Switzerland(n=10) TD=7246 ybp
Hungary(n=7) TD=5952 ybp
Romania(n=12) TD=11199 ybp
Caucasus(n=32) TD=12217 ybp
Bashkirs(n=29) TD=1624 ybp
Pakistan(n=5) TD=14493
Turkey(n=58) TD=11057 ybp
Italy(n=14) TD=9526 ybp
Poland(n=7) TD=3106 ybp

Those dates were used to construct the map you provided:

http://rokus01.files.wordpress.com/2010/09/l23.png

As you can see the reason why it appears as if Northern Iran, Afghanistan and Pakistan have such an old date, is due to the anomalous results from Pakistan, which are likely due to the small sample size. However given that we have no data from Iran, at least not from Myres et al(2010), it is really hard to come to any reasonable conclusion that L23 originated in Northern Mesopotamia. Something else to look at, is that the TD of Romania, and of Turkey are very similar, and this is something I observed in my own calculations of Variance for L23(xL51). However, my results differ from theirs, in that I calculate the modal in a locus basis, whereas they do it finding the median haplotype per population.  If I was forced to postulate a hypothesis based on the data published by Myres et al(2010); I would say that given the relatively significant presence of R1b-M269(xL23) in the Balkans, and the relatively significant variance of R1b-L23(xL51) in Romania, that L23 was born somewhere near Romania either to the West of it, or to the East of it.



I am glad you commented on my post because I thought there would be weaknesses in the Myres map.  There are some commonalities though.  I am not surprised that there is a similarity in high variance in Turkey and countries immediately west of the Black Sea like Romania as the areas are known to be connected by the Neolithic cultures like Hamangia and others in the area.  its probably that very connection that brought cattle dairy farming into Europe shortly before 5000BC.  There are lots of other less well understood connections between NE Anatolia and Thrace  Archeolgically it is easier to see the direction of flow as Anatolia to Bulgaria and Romania.  If the variance is similar perhaps L23* occurred pretty well at that moment in time as the movements were about to take place.

On the other hand, the L23* map from Rokus's site does seem to make variance higher in western Turkey and if you took that at face value (which I probably shouldnt) the only way of  linking the high variance in west Anatolia to the Romania area leaving the high variance area (without getting in a boat) would actually by going around the east side of the Black Sea and through southern Russia/Ukraine.  So, the possibility that it could have actually got to Romania by a round about route like that should be borne in mind.  The possibility that L23 actually passed into the steppes and reached the area to the west of the Black Sea from the steppes cannot be ruled out.  It is noticeable that the Aegean coast itself around Turkey, Greece etc is in a low variance area for L23* which doesnt really point to that particular route.   
 
I find the M269* west Balkans aspect very interesting though although I find it harder to work out a way of squaring it with population movements I know of.   

 
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JeanL
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« Reply #139 on: May 17, 2012, 04:22:02 PM »

I thought it would be interesting to compare the newly released data for European G-P15+(Rootsi.et.al.2012) to the data for European R1b-L23+(Myres.et.al.2010). Rootsi.et.al.2012 uses 19 STRs, but Myres.et.al.2010 uses only 10 STRs, fortunately enough, they intersect in those 10 STRs, unfortunately Rootsi.et.al.2012 reported having some problems with DYS19, and I too encounter some problems using DYS19, so the intersected database consisted of 9 STRs:

DYS388, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS439, DYS461.

The sample size for European G-P15+ was 189, whereas the sample size for European R-L23+ was 812. So in order to test whether there was a bias caused by the sample size difference, I ran ten experiments where I randomly drew 189 European R-L23+ haplotypes, and calculated the variance of the random sample. I included all the data, so one can see the variance of the European R-L23+ using all 812 haplotypes, and the variances calculated using 189 randomly drawn haplotypes for each one of the ten experiments. At the end I took the average variance of the 10 random samples, and I also calculated the standard deviation.

Here are the results:



http://i1133.photobucket.com/albums/m582/jeanlohizun/Myresetal2010Rootsietal2012-VarianceComparisonG-P15vsR-L23.jpg

What stands out, is that the variance of European R-L23+ is about ~0.74 that of European G-P15+. G-P15+ has been found earliest in a Cardial site in Avellaner, Catalonia dating back to 5000 BC. If fix the TMRCA of European G-P15+ as being at least 7000 ybp, then this yields a TMRCA of at least 5100 ybp (3089 BC) for European R-L23+.

PS: I did not try to correct for back mutations, because I wasn't calculating TMRCA but comparing the relative variance of R-L23+ to G-P15+ in Europe. So, I am well aware that there might be back mutations that have occurred in R-L23+, but there are also back mutations that have occurred in G-P15+. I'm assuming that the correcting factors would be close enough to each other as to assume their ratio would be 1.
« Last Edit: May 17, 2012, 04:31:54 PM by JeanL » Logged
Mark Jost
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« Reply #140 on: May 17, 2012, 04:42:40 PM »



Would you mind doing the same calculations in all the P15+(G2a+) haplotypes found in the latest study published about Haplogroup G.

The haplotypes are found on Supplementary Table-3.

http://www.nature.com/ejhg/journal/vaop/ncurrent/suppinfo/ejhg201286s1.html

Ok, here they are.  I removed Hts with dual, missing, or obvious errors (ie -9) STR alleles in the spread sheet.

Modified KenN Gen111T using
Distinguishing the co-ancestries of haplogroup G
Siiri Rootsi Etal
http://www.nature.com/ejhg/journal/vaop/ncurrent/suppinfo/ejhg201286s1.html
15 marker study using 15 Markers.

G-P15 and P16

 
YrsPerGen*   Count   AGE   Generations   YBP   Founder   Generations   YBP      
25   N=15   G-P15 GA coal=   199.9   4,998.2   GA=   269.0   6,726.2      
                           
25   N=107   G-P16 GB coal=   208.3   5,207.5   GB=   221.3   5,532.5      
                           
TMRCA      Founder                     
25      GAB=   398.9   9,972.1            

G-P15 and L497

 
YrsPerGen*   Count   AGE   Generations   YBP   Founder   Generations   YBP      
25   N=15   G-P15 GA coal=   199.9   4,998.2   GA=   269.0   6,726.2      
                           
25   N=62   G-L497 GB coal=   83.3   2,081.8   GB=   94.5   2,361.6      
                           
TMRCA      Founder                     
25      GAB=   275.0   6,874.2            



G-P15 and L91

 
YrsPerGen*   Count   AGE   Generations   YBP   Founder   Generations   YBP      
25   N=15   G-P15 GA coal=   199.9   4,998.2   GA=   269.0   6,726.2      
                           
25   N=29   G-L91 GB coal=   78.4   1,959.0   GB=   101.0   2,524.5      
                           
TMRCA      Founder                     
25      GAB=   304.6   7,614.7            



G-P15 and M285

 
YrsPerGen*   Count   AGE   Generations   YBP   Founder   Generations   YBP         
25   N=15   G-P15 GA coal=   199.9   4,998.2   GA=   269.0   6,726.2         
                              
25   N=17   G-M285 GB coal=   171.0   4,274.5   GB=   251.9   6,296.8         
                              
TMRCA      Founder                        
25      GAB=   395.7   9,891.7            


G-P15 and PM377

 
YrsPerGen*   Count   AGE   Generations   YBP   Founder   Generations   YBP      
25   N=15   G-P15 GA coal=   199.9   4,998.2   GA=   269.0   6,726.2      
                           
25   N=23   G-M377 GB coal=   70.3   1,758.4   GB=   83.5   2,086.3      
                           
TMRCA      Founder                     
25      GAB=   389.0   9,725.0            

G-P15 and M406
 
YrsPerGen*   Count   AGE   Generations   YBP   Founder   Generations   YBP      
25   N=15   G-P15 GA coal=   199.9   4,998.2   GA=   269.0   6,726.2      
                           
25   N=35   G-M406 GB coal=   143.0   3,574.7   GB=   183.5   4,587.7      
                           
TMRCA      Founder                     
25      GAB=   419.4   10,484.6            



G-P15 and M426

 
YrsPerGen*   Count   AGE   Generations   YBP   Founder   Generations   YBP      
25   N=15   G-P15 GA coal=   199.9   4,998.2   GA=   269.0   6,726.2      
                           
25   N=4   G-M426 GB coal=   4.6   115.4   GB=   6.2   153.8      

TMRCA      Founder                     
25      GAB=   302.8   7,570.9            



G-P15 and M485

 
YrsPerGen*   Count   AGE   Generations   YBP   Founder   Generations   YBP      
25   N=15   G-P15 GA coal=   199.9   4,998.2   GA=   269.0   6,726.2      
                           
25   N=4   G-M485 GB coal=   81.5   2,037.9   GB=   104.6   2,614.6      
                           
TMRCA      Founder                     
25      GAB=   413.5   10,337.3            

G-P15 and G-M527

 
YrsPerGen*   Count   AGE   Generations   YBP   Founder   Generations   YBP      
25   N=15   G-P15 GA coal=   199.9   4,998.2   GA=   269.0   6,726.2      
                           
25   N=30   G-M527 GB coal=   89.4   2,235.2   GB=   116.5   2,912.0      
                           
TMRCA      Founder                     
25      GAB=   273.9   6,846.4            


G-P15 and P20

 
YrsPerGen*   Count   AGE   Generations   YBP   Founder   Generations   YBP      
25   N=15   G-P15 GA coal=   199.9   4,998.2   GA=   269.0   6,726.2      
                           
25   N=7   G-P20 GB coal=   150.7   3,766.5   GB=   228.5   5,712.6      
                           
TMRCA      Founder                     
25      GAB=   426.0   10,651.0            


G-P15 and P303

 
YrsPerGen*   Count   AGE   Generations   YBP   Founder   Generations   YBP      
25   N=15   G-P15 GA coal=   199.9   4,998.2   GA=   269.0   6,726.2      
                           
25   N=58   G-P303 GB coal=   142.3   3,558.1   GB=   172.3   4,306.4      
                           
TMRCA      Founder                     
25      GAB=   294.4   7,360.7            


G-P15 and Page19

 
YrsPerGen*   Count   AGE   Generations   YBP   Founder   Generations   YBP      
25   N=15   G-P15 GA coal=   199.9   4,998.2   GA=   269.0   6,726.2      
                           
25   N=12   G-Page19 GB coal=   91.8   2,294.2   GB=   112.8   2,819.7      
                           
TMRCA      Founder                     
25      GAB=   396.1   9,902.2            


G-P15 and U1

 
YrsPerGen*   Count   AGE   Generations   YBP   Founder   Generations   YBP      
25   N=15   G-P15 GA coal=   199.9   4,998.2   GA=   269.0   6,726.2      
                           
25   N=118   G-U1 GB coal=   126.0   3,150.2   GB=   149.5   3,738.1      
                           
TMRCA      Founder                     
25      GAB=   276.4   6,909.8            



AND Just for Fun:   G-P15 and R1b-L21

 
YrsPerGen*   Count   AGE   Generations   YBP   Founder   Generations   YBP      
25   N=15   G-P15 GA coal=   199.9   4,998.2   GA=   269.0   6,726.2      
                           
25   N=648   R-L21 GB coal=   105.0   2,624.0   GB=   113.7   2,843.4                           
                        
TMRCA      Founder                     
25      GAB=   935.4   23,385.5            


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)
JeanL
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« Reply #141 on: May 17, 2012, 04:48:19 PM »

Ok, here they are.  I removed Hts with dual, missing, or obvious errors (ie -9) STR alleles in the spread sheet.
 

Thanks!!!

Yeah, I also removed the samples that were missing some STRs, and I also noticed the -9 thing, I thought about changing it to 9, but then I just deleted it. It made  me laugh a little, how does one get -9 repeats?
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alan trowel hands.
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« Reply #142 on: May 17, 2012, 04:54:08 PM »

As for the route to the west, one thing noticeable is that once west of Romania the variance of L23* is much lower north of the Balkans.  It is also noticeable that the Aegean coast itself around Turkey, Greece etc is in a low variance area for L23* which doesnt really point to that particular route.   That would seem (unless some massive jump by boat was done) that the route was north of Aegean Greece and south of the Dabube i.e. the Balkans.  The Balkans at least have L23*  variance equal to the norm for the west Med.  So you would have to think Occam's Razor favours a route through the Balkans to the west and some sort of sail along the Adriatic and along the Med. or perhaps a crawl along the southern fringe of the Alps.  L23* variance areas that are at least equal to the west Med. only overlap with L51* distribution at the head of the Adriatic.  Pehaps the west Balkan M269* arrived from somewhere like Romania as minority fellow travellors with L23* and L51* occurred in the north-west Balkans.

 
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« Reply #143 on: May 17, 2012, 05:04:48 PM »

Nice work Mark.  It is interesting that the G subclades appear in a wider neolithic time-frame.

One thing about R1b M269* and everything M269+ is the dates almost always come out to the 3rd millenium and later on Ken's Generations7 for 67 marker haplotypes.  
« Last Edit: May 17, 2012, 05:07:11 PM by MHammers » Logged

Ydna: R1b-Z253**


Mtdna: T

alan trowel hands.
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« Reply #144 on: May 17, 2012, 05:18:29 PM »

I thought it would be interesting to compare the newly released data for European G-P15+(Rootsi.et.al.2012) to the data for European R1b-L23+(Myres.et.al.2010). Rootsi.et.al.2012 uses 19 STRs, but Myres.et.al.2010 uses only 10 STRs, fortunately enough, they intersect in those 10 STRs, unfortunately Rootsi.et.al.2012 reported having some problems with DYS19, and I too encounter some problems using DYS19, so the intersected database consisted of 9 STRs:

DYS388, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS439, DYS461.

The sample size for European G-P15+ was 189, whereas the sample size for European R-L23+ was 812. So in order to test whether there was a bias caused by the sample size difference, I ran ten experiments where I randomly drew 189 European R-L23+ haplotypes, and calculated the variance of the random sample. I included all the data, so one can see the variance of the European R-L23+ using all 812 haplotypes, and the variances calculated using 189 randomly drawn haplotypes for each one of the ten experiments. At the end I took the average variance of the 10 random samples, and I also calculated the standard deviation.

Here are the results:



http://i1133.photobucket.com/albums/m582/jeanlohizun/Myresetal2010Rootsietal2012-VarianceComparisonG-P15vsR-L23.jpg

What stands out, is that the variance of European R-L23+ is about ~0.74 that of European G-P15+. G-P15+ has been found earliest in a Cardial site in Avellaner, Catalonia dating back to 5000 BC. If fix the TMRCA of European G-P15+ as being at least 7000 ybp, then this yields a TMRCA of at least 5100 ybp (3089 BC) for European R-L23+.

PS: I did not try to correct for back mutations, because I wasn't calculating TMRCA but comparing the relative variance of R-L23+ to G-P15+ in Europe. So, I am well aware that there might be back mutations that have occurred in R-L23+, but there are also back mutations that have occurred in G-P15+. I'm assuming that the correcting factors would be close enough to each other as to assume their ratio would be 1.

Well a date of European L23* of c. 3100BC give or take some centuries is very close to the models a lot of people are coming up with using variance for L23 derived clades.  I cant see any evidence suggesting a movement into Europe from south of the Black Sea at that time but there was clearly movement into the east end of the Danube from the steppes.  So perhaps my earlier guessology (using the L23* variance map) that L23* went from a high variance area (eastern Turkey, Armenia?) through or around the Caucuses into the steppe and became part of the mix there among the steppe groups and then were swept into the Lower Danube area etc.  Which is very Kurgan modelesque.  It certainly looks from the L23* variance map that L23* most likely got to Romania c. 3000BC through a route like that.  I am suprised I have never really looked at that map with my brain in gear before. However it seems clear to me that variance drops off in western Turkey and and drops way off on the Aegean coasts and a route for L23* into Romania by a circuitous route round the east and north shore of the Black Sea actually makes more sense.  

I dont know what that would all mean in terms of IE.  it could be fitted into the Kurgan theories with dairy farmers inputting into the steppes and teaching the hunters crucial aspects of what would become PIE culture.  So, PIE society was a blend of two strands and without one or the other it simply wouldnt have become the PIE society that has been reconstructed.  
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« Reply #145 on: May 17, 2012, 05:55:42 PM »

I thought it would be interesting to compare the newly released data for European G-P15+(Rootsi.et.al.2012) to the data for European R1b-L23+(Myres.et.al.2010). .....
What stands out, is that the variance of European R-L23+ is about ~0.74 that of European G-P15+. G-P15+ has been found earliest in a Cardial site in Avellaner, Catalonia dating back to 5000 BC. If fix the TMRCA of European G-P15+ as being at least 7000 ybp, then this yields a TMRCA of at least 5100 ybp (3089 BC) for European R-L23+....  
That's a very illustrative comparison. No matter what the problems there might be with STR issues, there other subclades, i.e. G-P15, appears relatively older (or at least more diverse) in Europe than R-L23.
« Last Edit: May 18, 2012, 09:03:34 AM by Mikewww » Logged

R1b-L21>L513(DF1)>S6365>L705.2(&CTS11744,CTS6621)
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« Reply #146 on: May 17, 2012, 05:58:50 PM »

and a futher thought is if L23* moved out of northern Mesopotamia and was already in the steppes, Anatolia and the Balkans in three seperated groups in say 4000BC then that also bears a bit of a parallel to the PIE/Anatolian split.

Anyway before getting too complicated, I would ask for opinions on this - if L23" was one of the groups (presimably a dairy element infiltratng) in the steppes say 4000BC and they were among R1a hunters morphing inot nomadic pastoralists then who is to say which one of the two groups actually spoke IE first?  Perhaps the north Mesopotamian L23 pushed into Anatolia (and maybe also crossing the Bosphorus) in one branch and another headed through the Caucuses into the steppes. That sort of scenario does bear some resemblence to the linguistic one where the Anatolian branch split off early from the group who were to become PIE.   I am not saying that happened but I cant see any reasson why it is not an option. 

I just want to add a couple of thoughts to it:

1-This is a paragroup, which is L23(xM412/L51), I too did the calculations of variance for the paragroup L23*, and found it to be the oldest at the Caucasus, however, this was only observed when all Caucasian populations were sampled as a whole, individually, the variance decayed greatly.  You can find more about it here: http://i1133.photobucket.com/albums/m582/jeanlohizun/Myresetal2010Herreraetal2010L23xL51data.jpg

2-The graph you provided shows Isoclines based on the data collected from Table-S2, more specifically it shows the Coalescent times rather than the variance. Myres et al(2010) used the evolutionary rate to calculate those coalescence times. The main problem here, is that the data for L23* is as follows:

Greece(n=15) TD=6763 ybp
Slovakia(n=10) TD=5153 ybp
Switzerland(n=10) TD=7246 ybp
Hungary(n=7) TD=5952 ybp
Romania(n=12) TD=11199 ybp
Caucasus(n=32) TD=12217 ybp
Bashkirs(n=29) TD=1624 ybp
Pakistan(n=5) TD=14493
Turkey(n=58) TD=11057 ybp
Italy(n=14) TD=9526 ybp
Poland(n=7) TD=3106 ybp

Those dates were used to construct the map you provided:

http://rokus01.files.wordpress.com/2010/09/l23.png

As you can see the reason why it appears as if Northern Iran, Afghanistan and Pakistan have such an old date, is due to the anomalous results from Pakistan, which are likely due to the small sample size. However given that we have no data from Iran, at least not from Myres et al(2010), it is really hard to come to any reasonable conclusion that L23 originated in Northern Mesopotamia. Something else to look at, is that the TD of Romania, and of Turkey are very similar, and this is something I observed in my own calculations of Variance for L23(xL51). However, my results differ from theirs, in that I calculate the modal in a locus basis, whereas they do it finding the median haplotype per population.  If I was forced to postulate a hypothesis based on the data published by Myres et al(2010); I would say that given the relatively significant presence of R1b-M269(xL23) in the Balkans, and the relatively significant variance of R1b-L23(xL51) in Romania, that L23 was born somewhere near Romania either to the West of it, or to the East of it.

It is not hard to imagine.  Although, again, I am not suggesting N Mesopotamia as its point of origin, considering the lack of sampling from several of the minority populations of the general region, including the two most significant Assyrian churches.  Not to mention, certain areas of Europe, and other parts of the world.  Plus, I still have a feeling that this is not its origin.  I would look to the Levant, the Caucasus, Armenian Highland, and perhaps even NW Iran first.   

N Mesopotamian  Nine of the ten STRs from Myres et al. 

Code:
393 390 19 391 388 439 389 392 389
13 24 14 10 12 12 14 13 30
13 24 14 10 12 12 14 13 30
13 24 14 10 12 12 14 13 30
13 24 14 10 12 12 14 13 30
13 24 14 10 12 12 14 13 30
13 24 14 10 12 12 14 13 30
12 23 12 11 12 12 13 14 28
12 24 13 11 12 13 13 14 30
12 24 13 10 12 12 14 13 30
12 24 14 10 12 12 13 14 29
12 24 14 11 12 12 13 13 29
12 24 14 10 12 12 12 13 26
12 24 15 11 12 12 12 14 27
12 25 14 11 12 12 12 14 28
12 25 14 10 12 12 13 14 29
12 26 14 11 12 13 13 14 29
13 24 14 10 12 11 14 13 30
13 24 14 11 12 12 14 13 30
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« Reply #147 on: May 17, 2012, 06:09:08 PM »

It is not hard to imagine.  Although, again, I am not suggesting N Mesopotamia as its point of origin, considering the lack of sampling from several of the minority populations of the general region, including the two most significant Assyrian churches.  Not to mention, certain areas of Europe, and other parts of the world.  Plus, I still have a feeling that this is not its origin.  I would look to the Levant, the Caucasus, Armenian Highland, and perhaps even NW Iran first.   

N Mesopotamian  Nine of the ten STRs from Myres et al. 

Code:
393 390 19 391 388 439 389 392 389
13 24 14 10 12 12 14 13 30
13 24 14 10 12 12 14 13 30
13 24 14 10 12 12 14 13 30
13 24 14 10 12 12 14 13 30
13 24 14 10 12 12 14 13 30
13 24 14 10 12 12 14 13 30
12 23 12 11 12 12 13 14 28
12 24 13 11 12 13 13 14 30
12 24 13 10 12 12 14 13 30
12 24 14 10 12 12 13 14 29
12 24 14 11 12 12 13 13 29
12 24 14 10 12 12 12 13 26
12 24 15 11 12 12 12 14 27
12 25 14 11 12 12 12 14 28
12 25 14 10 12 12 13 14 29
12 26 14 11 12 13 13 14 29
13 24 14 10 12 11 14 13 30
13 24 14 11 12 12 14 13 30


Where  did you get those haplotypes, and to what haplogroup(i.e. M269(xL23), L23(xL51), etc) do they belong? I certainly have analyzed Myres.et.al.2010 deeply and there is nothing on Iran, the only haplotype listed on Supplementary Table-3 from Iran is 1-R1b-M269(xL23), and that is about it.
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Mark Jost
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« Reply #148 on: May 17, 2012, 06:16:28 PM »

Ok, here they are.  I removed Hts with dual, missing, or obvious errors (ie -9) STR alleles in the spread sheet.
 

Thanks!!!

Yeah, I also removed the samples that were missing some STRs, and I also noticed the -9 thing, I thought about changing it to 9, but then I just deleted it. It made  me laugh a little, how does one get -9 repeats?

Not once but three or four -9's..... has to be  typo but I didnt wish to assume as there was enough other HTs to work with.  I wasnt sure of how to consolidate the mutli alleles reported in DYS19. Is it alway the lowest or the highest number of the set? Do you know?
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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)
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« Reply #149 on: May 17, 2012, 06:23:16 PM »

It is not hard to imagine.  Although, again, I am not suggesting N Mesopotamia as its point of origin, considering the lack of sampling from several of the minority populations of the general region, including the two most significant Assyrian churches.  Not to mention, certain areas of Europe, and other parts of the world.  Plus, I still have a feeling that this is not its origin.  I would look to the Levant, the Caucasus, Armenian Highland, and perhaps even NW Iran first.   

N Mesopotamian  Nine of the ten STRs from Myres et al. 

Code:
393 390 19 391 388 439 389 392 389
13 24 14 10 12 12 14 13 30
13 24 14 10 12 12 14 13 30
13 24 14 10 12 12 14 13 30
13 24 14 10 12 12 14 13 30
13 24 14 10 12 12 14 13 30
13 24 14 10 12 12 14 13 30
12 23 12 11 12 12 13 14 28
12 24 13 11 12 13 13 14 30
12 24 13 10 12 12 14 13 30
12 24 14 10 12 12 13 14 29
12 24 14 11 12 12 13 13 29
12 24 14 10 12 12 12 13 26
12 24 15 11 12 12 12 14 27
12 25 14 11 12 12 12 14 28
12 25 14 10 12 12 13 14 29
12 26 14 11 12 13 13 14 29
13 24 14 10 12 11 14 13 30
13 24 14 11 12 12 14 13 30


Where  did you get those haplotypes, and to what haplogroup(i.e. M269(xL23), L23(xL51), etc) do they belong? I certainly have analyzed Myres.et.al.2010 deeply and there is nothing on Iran, the only haplotype listed on Supplementary Table-3 from Iran is 1-R1b-M269(xL23), and that is about it.

The haplotypes are from the Assyrian project, Aramaic project, and one Assyrian man from SMGF.  Please let me point out that none of these haplotypes are "from" Iran, regardless of what may be listed as country of origin.  We have lived in many countries over the last several centuries, for various reasons.  However, if you follow the autosomal projects (Dodecad, Eurogenes, Harappa), one thing is exceedingly clear, our genes are principally northern Mesopotamian (basically, what is today extreme N Iraq).  And this does not even begin to touch on the linguistic, cultural, and other ties to the region, supporting the same conclusion.

The men with DYS393=13 are most similar to the Alawite men of NW Syria.  Who in turn are most similar to both Assyrians and Druze.  The Druze are the carriers of what appears to be the AMH.  I do not mean to spam the forum with this data, over and over again, but, this is what I am referring to:

Atlantic Modal Haplotype
13-24-14-11-11-14-12-12-12-13-13-29

Druze R1b modal and secondary haplotype (Shlush et al.)
13-24-14-11-xx-xx-12-12-xx-13-13-29
12-24-14-11-xx-xx-12-12-xx-13-13-29

Alawite R1b modal and secondary haplotype (Dönbak et al.)
13-24-14-11-11-15-xx-xx-xx-14-13-30
13-24-14-11-11-15-xx-xx-xx-13-13-29

Assyrian R1b modal haplotype (FTDNA)
13-24-14-10-11-14-12-12-12-14-13-30
« Last Edit: May 17, 2012, 06:23:55 PM by Humanist » Logged

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