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alan trowel hands.
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« Reply #25 on: January 20, 2011, 08:15:14 PM »

One thing I find interesting is that some calculations find S116* to be younger than U152.  That (unless its down to confidence intervals etc) suggests the possibility that the lines that are negative for other SNPs have a common ancestor that is significantly more recent than the S116 SNP, at least by quite a few centuries.  This implies that the early shared ancestral lines of these L21/U152 etc negative S116 group of lineages did not prosper at first.  There seems to be a period of less success in the window between S116 and I152 SNPs.  Possibly it is all a case of the seed falling on fertile ground.  The U152 and L21 lines simply stumbled upon opportunity.  I am not sure about U152 but in a mid Neolithic scenario L21 would have found some virgin territory settled only by hunters around coastal northern France.. In a similar period it is possible that U152 could have benefited from the poorly Neolithicised area around the Alps and in central France where neither the LBK or the Cardial waves had reached with any strength. It is also true that much of Iberia away from the south and west coasts was remote from the main Cardial waves there.  Finally, most of the coastal areas of what is now Germanic Europe was also not Neolithicised until the middle Neolithic.  

Maybe the clade explosion we see among L11 is down to the sudden secondary expansion of Neolithic peoples. Some think France (which was only partly Neolthicised by LBK and Cardial cultures) had a major period of secondary expansion in the middle Neolithic that was responsible for the first true farming cultures in north coastal and part of interior France.  I think I recall it being suggested that these French middle Neolithic groups expansion could have also impacted into interior and northern Iberia and parts of Italy.  Is it possible that this is the link with the peak variance for some clades falling into France?  I certainly struggle to find other periods where France stands out as some sort of centre of expansion.  

The middle Neolithic seems to have been a period where good climate and clever adaptation of farming practices allowed expansion away from the limited areas the rather choosey LBK (they like Loess soils or failing that sands and gravel subsoils) and Cardial settlers had settled (and failed to expand beyond for many centuries). The middle Neolithic was the 2nd post-hunter-gatherer demographic window after the 'spread of farming 1000 years or so earlier. So if you look to match demographic explosions in DNA with windows of opportunity then the middle Neolithic is certainly a major one.  It has the advantages of being 1-2000 years later than the spread of farming which I suppose closes some of the disparity with the variance dates suggested.  

The geography of the places where these opportunities were highest in terms of territory that was essentially virgin with regards to fully developed farming cultures is interesting too - the isles, north and NW coastal fringe France, much of interior France, the low Countries, the Alpine area of Europe (including parts of north Italy), Iberia away from the south or west coasts, Denmark etc.  These area all areas where L11 clades are elevated.  In terms of the map of Europe and even looking at subdivisions of it, it seems R1b1b2 (mainly L11 clades) increases where a strong farming economy was only established in the middle Neolithic.

So, did L11 suddenly explode with the middle Neolithic window of opportunity and create the areas of elevated R1b1b2 we see now?  If so, what were it roots?  There is no strong evidence that the middle Neolithic groups were outsiders.  I think in general these groups are seen as descendants of LBK groups who had adapted to more marginal conditions and perhaps absorbed some local hunters.  


« Last Edit: January 20, 2011, 08:20:08 PM by alan trowel hands. » Logged
alan trowel hands.
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« Reply #26 on: January 20, 2011, 08:33:44 PM »

...and I forgot to say.  The correlation between elevated R1b1b2 (well L11 anyway) and areas that were not settled by real farming cultures until the middle Neolithic was misinterpreted as down to hunter gatherer survival a few years ago before the phylology of R1b1b2 was better understood.  You can see how that would come about.  The map of R1b1b2 frequency is almost the reverse of the map of early Neolithic cultures.  R1b1b2 tends to be strongest where the early Neolithic didnt spread to.  So people put 2 and 2 together and got R1b=hunters.  However what I am now saying is that while the observation that R1b1b2 strength is almost inversely correlated with early Neolithic settlement is essentially true, the real reason is not hunter-gatherer survival but middle Neolithic settlement. 

..and the reason why L11 clades are poorly correlated with the LBK spread?  They didnt exist at the time.  Obviously to expand in the middle Neolithic L11 or its ancestors had to have been on the scene and to have been in a particularly advantageous spot.
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MHammers
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« Reply #27 on: January 20, 2011, 08:47:38 PM »

Here are some calculations I ran using Ken N.'s Generations5 interclade calculator.  The data comes from the Yahoo P312 project.  Thanks to Mikewww, Ken, and Vince V. for making these resources available.  These are all 67 marker ht's with only 50 used in the spreadsheet.

All P312 (Generations/Sigma generations , Gx30=years ago , n=)
France - 149/11, 4440, 93
Iberia - 129/9.1, 3870, 66
Germany - 126/11, 3780, 103
Scandinavia - 113/10, 3390, 48
Alpine(Switzerland, North Italy, Austria) - 111/8.7, 3330, 42)

Here are some interclade estimates using W. Europe P312*, n=105, as the ancestor clade or sample A on the spreadsheet.  The following were entered seperately as sample B.  I'm still trying to grasp the interclade concept, so hopefully this is the right approach.

Iberia L176 - 132/42, 3960, 8
France L21 - 136/43, 4080, 27
Iberia L21 - 126/41, 3780, 16
France U152 - 163/50, 4890, 26
Alpine U152 - 133/43, 3990, 32

I plan on running some more later.

« Last Edit: January 21, 2011, 01:37:27 AM by MHammers » Logged

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« Reply #28 on: January 21, 2011, 08:32:28 PM »

Some more TMRCA's using 30 yrs. per generation.  I intend to look at the British Isles, once I can modify my copy of the spreadsheet to accommodate the much larger samples.

All P312
Eastern Europe G-127/10, 3810, n-28

All L21
France L21 136/20, 4080, n-27
Iberia 134/17, 4020,  n-16
Germany 127/14, 3810, n-26
E Eur 104/16, 3120, n-16
Scandinavia 101/12, 3030, n-22

All U152
Low Countries 157/15, 4710, n-10
France 151/9.5, 4530, n-26
Iberia 135/21, 4050, n-6
Scandinavia 135/16, 4050, n-6
South Italy 133/20, 3990, n-8
E Eur 127/10, 3810, n-30
Germany 125/10, 3750 n-42
Alpine 116/10, 3480, n-32

All L176
Iberia 115/14, 3450, n-8
Germany 112/15, 3360, n-7
France 112/13, 3360, n-14

Interclade L51*/L11* (Ht 35 project)
Mostly of Central and Western Europe descent 167/51, 5010, n-12/35

The oldest so far.  If you add  or subtract the sigma you get between 3480-6650 years which spans from the middle neolithic to the bronze age.

Interclade L11*/Western Europe P312(includes P312, P312*, and P312** from Yahoo project)
136/44, 4080, n-35/105
« Last Edit: January 21, 2011, 08:34:50 PM by MHammers » Logged

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« Reply #29 on: January 22, 2011, 12:01:00 AM »

Here are some calculations I ran using Ken N.'s Generations5 interclade calculator.  The data comes from the Yahoo P312 project.  Thanks to Mikewww, Ken, and Vince V. for making these resources available.  These are all 67 marker ht's with only 50 used in the spreadsheet.

All P312 (Generations/Sigma generations , Gx30=years ago , n=)
France - 149/11, 4440, 93
Iberia - 129/9.1, 3870, 66
Germany - 126/11, 3780, 103
Scandinavia - 113/10, 3390, 48
Alpine(Switzerland, North Italy, Austria) - 111/8.7, 3330, 42)

Here are some interclade estimates using W. Europe P312*, n=105, as the ancestor clade or sample A on the spreadsheet.  The following were entered seperately as sample B.  I'm still trying to grasp the interclade concept, so hopefully this is the right approach.

Iberia L176 - 132/42, 3960, 8
France L21 - 136/43, 4080, 27
Iberia L21 - 126/41, 3780, 16
France U152 - 163/50, 4890, 26
Alpine U152 - 133/43, 3990, 32

I plan on running some more later.



Sorry, I do not understand these figures. Could you knidly explain what the three sets of numbers represent, and what they signify?
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« Reply #30 on: January 22, 2011, 11:17:55 AM »

@GoldenHind
The larger number is the generations to the most recent common ancestor for that sample.  The second smaller number is the sigma or standard deviation in generations (for example + or - 500 years).  The third number is actual years, generations x 30 yrs. per generation.  N= sample size.

I also ran a revised interclade for U152 which I think the gives a much better estimation of its age.  The previous interclade for France only had a sample of 26 and contained undifferentiated and downstream (U152 only) types.  The P312 sample had 6 undifferentiated, but no known downstream types.  This time, I used 99 P312* and P312** with 93 U152* and U152**.  This is all of the Western Europe sample which has the highest variance and diversity, so it is a better candidate than say Eastern Europe for the ancestral population.  By using the * and ** members it should be a better representation for the ancestral populations without the undifferentiated members who may actually be L21, L176, L2, etc.
 
I got G=137/44 or 4110 years which is much more in line with the other estimates.  With France having the highest variance and intraclade for U152, it is likely the origin is there or near the Low countries. A better explanation is, if I try to find the age of L21 from somewhere and include M222, a younger subclade with a distinct haplotype from most other L21, it will put the age of L21 higher than it actually is in an interclade estimate.
« Last Edit: January 22, 2011, 11:52:20 AM by MHammers » Logged

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alan trowel hands.
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« Reply #31 on: January 22, 2011, 03:11:02 PM »

The L21 date is about 500 years too young if a beaker model is used.  The latest L21 could have emerged from S116 if is associated with the beaker dispersal is 2500BC. I think Ken Nordvedt has arrived at even younger dates.  So, it does make you wonder if the variance methodology needs a bit of recalibration. 
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« Reply #32 on: January 22, 2011, 11:28:01 PM »

The L21 date is about 500 years too young if a beaker model is used.  The latest L21 could have emerged from S116 if is associated with the beaker dispersal is 2500BC. I think Ken Nordvedt has arrived at even younger dates.  So, it does make you wonder if the variance methodology needs a bit of recalibration.  

Most of the dates seem to hover around 2000 BC.  L11+ was probably among the eastern Beaker people, before that either "old Europe" farmers or Yamnaya tribes.  See the Dosideri (sp?) study on Bell Beaker dental traits which explains an earlier western Beaker people (perhaps Hg's E, I, G, J, and T) moving east into south France, Switzerland, and maybe Hungary.  I think if the Yamnaya people were R1b in Hungary at the time they became absorbed by this "Beaker interaction sphere", then spread north and west in the later Beaker movements to Scandinavia and the British Isles via the Rhine.  The intermarriage of these two people may have created the distinct Beaker physical type which was previously unknown.  The origin of Beaker in Iberia in 2900 BC or so may have been the result of the secondary products revolution coming from the east before the main migrations of Yamnaya people around 3100.
« Last Edit: January 22, 2011, 11:44:21 PM by MHammers » Logged

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Mike Walsh
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« Reply #33 on: August 08, 2011, 05:11:23 PM »

I decided to look at a by country perspective of R-P312 "All" and get to some of the countries/regions where our sample sizes are not that large. To do that I backed down to accept 37 length haplotypes or greater. Looking at just the 25 non-multi-copy markers of the 1st 37 I came up with the following relative variances.

I was startled a bit to find East/Central Europe (anything east of Germany/Switz/Austria but not the Balkans nor SW Asia) came up higher than France....   so I broke it out as best I could, but it didn't change the ranking....


Hungary_____________:  Var=1.31   (N=15)
Baltic States_______:  Var=1.24   (N=15)
Belarus/Russia/Ukrai:  Var=1.23   (N=26)   
Poland______________:  Var=1.15   (N=26)
France______________:  Var=1.12   (N=188)
Czech Rep.__________:  Var=1.10   (N=12)
England_____________:  Var=1.03   (N=540)
Nordic Area_________:  Var=1.02   (N=71)
Germany_____________:  Var=1.01   (N=181)
Switzerland_________:  Var=0.98   (N=43)
Italy_______________:  Var=0.96   (N=60)
Ireland_____________:  Var=0.94   (N=935)
Wales_______________:  Var=0.93   (N=91)
Iberia______________:  Var=0.92   (N=494)
Benelux Area________:  Var=0.91   (N=43)
Scotland____________:  Var=0.90   (N=463)
« Last Edit: August 08, 2011, 05:16:36 PM by Mikewww » Logged

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« Reply #34 on: August 08, 2011, 05:27:16 PM »

I decided to look at a by country perspective of R-P312 "All" and get to some of the countries/regions where our sample sizes are not that large. To do that I backed down to accept 37 length haplotypes or greater. Looking at just the 25 non-multi-copy markers of the 1st 37 I came up with the following relative variances.

I was startled a bit to find East/Central Europe (anything east of Germany/Switz/Austria but not the Balkans nor SW Asia) came up higher than France....   so I broke it out as best I could, but it didn't change the ranking....


Hungary_____________:  Var=1.31   (N=15)
Baltic States_______:  Var=1.24   (N=15)
Belarus/Russia/Ukrai:  Var=1.23   (N=26)   
Poland______________:  Var=1.15   (N=26)
France______________:  Var=1.12   (N=188)
Czech Rep.__________:  Var=1.10   (N=12)
England_____________:  Var=1.03   (N=540)
Nordic Area_________:  Var=1.02   (N=71)
Germany_____________:  Var=1.01   (N=181)
Switzerland_________:  Var=0.98   (N=43)
Italy_______________:  Var=0.96   (N=60)
Ireland_____________:  Var=0.94   (N=935)
Wales_______________:  Var=0.93   (N=91)
Iberia______________:  Var=0.92   (N=494)
Benelux Area________:  Var=0.91   (N=43)
Scotland____________:  Var=0.90   (N=463)


Interesting that there is still an east to west cline even at the 37 marker level.  It looks like there was a relatively early jump to England, maybe from the Rhine.
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« Reply #35 on: August 08, 2011, 10:04:41 PM »

 Very interesting, but it doesn't surprise me in the least.

As for the Balkans, do we really have a decent sampling there?. If you look at the various P312 subclade maps, there always seems to be a doughnut hole there. Is it because P312 is actually rarish there, or just because we don't have the data?
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« Reply #36 on: August 09, 2011, 06:40:23 PM »

Very interesting, but it doesn't surprise me in the least.

As for the Balkans, do we really have a decent sampling there?. If you look at the various P312 subclade maps, there always seems to be a doughnut hole there. Is it because P312 is actually rarish there, or just because we don't have the data?
We still don't have many R-P312 haplotypes from the Balkans, but I added the south of Italy together with Greece, Croatia, Algeria and Malta to result with this:

Eastern Med Europe__:  Var=0.90  (N=27)   

If I just look at the Balkans, this is all we get

Greece/Croatia______:  Var=0.85  (N=4)

I've never been able to figure out how a Mediterranean route into Europe worked for R-P312, at least when looking at the variance and the phylogenetic trail. It seems like the more samples and resolution, the more indications are that R-P312 moved east to west across the core of the continent.

This not to say that R-L23+ L11- and R-L11* didn't reach Italy and Iberia early, it's just that P312 seems to have come overland and seeped across the Alps into Italy (Cisalpine Gaul) rather than the other way around.
« Last Edit: August 09, 2011, 06:43:16 PM by Mikewww » Logged

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alan trowel hands.
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« Reply #37 on: August 14, 2011, 07:39:20 PM »

I decided to look at a by country perspective of R-P312 "All" and get to some of the countries/regions where our sample sizes are not that large. To do that I backed down to accept 37 length haplotypes or greater. Looking at just the 25 non-multi-copy markers of the 1st 37 I came up with the following relative variances.

I was startled a bit to find East/Central Europe (anything east of Germany/Switz/Austria but not the Balkans nor SW Asia) came up higher than France....   so I broke it out as best I could, but it didn't change the ranking....


Hungary_____________:  Var=1.31   (N=15)
Baltic States_______:  Var=1.24   (N=15)
Belarus/Russia/Ukrai:  Var=1.23   (N=26)   
Poland______________:  Var=1.15   (N=26)
France______________:  Var=1.12   (N=188)
Czech Rep.__________:  Var=1.10   (N=12)
England_____________:  Var=1.03   (N=540)
Nordic Area_________:  Var=1.02   (N=71)
Germany_____________:  Var=1.01   (N=181)
Switzerland_________:  Var=0.98   (N=43)
Italy_______________:  Var=0.96   (N=60)
Ireland_____________:  Var=0.94   (N=935)
Wales_______________:  Var=0.93   (N=91)
Iberia______________:  Var=0.92   (N=494)
Benelux Area________:  Var=0.91   (N=43)
Scotland____________:  Var=0.90   (N=463)


Very strongly east to west.  The main oddity is France IMO.  If it had been 1.0 or something then the whole pattern would be more logical.  Nevertheless, the general pattern is clear.  It is also true that L21 features that oddity of France having higher variance than Germany.  Certainly for S116 it spoils the otherwise fairly logical variance pattern. 
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