Correlating haplogroups with ancient admixture

sparkey

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3/4 Colonial American, 1/8 Cornish, 1/8 Welsh
Y-DNA haplogroup
I2c1 PF3892+ (Swiss)
mtDNA haplogroup
U4a (Cornish)
Eurogenes has recently explored a three-component admixture analysis based on ancient samples, in which the three components are named WHG (West European Hunter-Gatherer), EEF (Early European Farmer), and ANE (Ancient North Eurasian). This analysis can be applied to existing European populations. See here.

Based on existing ancient samples and analysis of modern samples, there's a strong indication that Haplogroup I was important in the source population(s) of WHG, and Haplogroup R (perhaps especially R1a?) was important in the source population(s) of ANE. But do these patterns still hold? Taking the breakdown from Eurogenes and the Y-DNA frequencies from Eupedia, I get the following scatter plots and basic regression lines:

9esy.png


Furthermore, we can see some interesting patterns when looking at the difference between haplogroup and component frequency population-by-population:

wi9n.png


What to take from this? Here are some of my takes:

  • Haplogroup I doesn't correlate with much of anything, with its strongest positive correlation being with WHG as we may expect, but even with that one, it is a weak correlation. This could be explained by the haplogroup being widespread in Europe early, but with several later expansions into non-WHG-dominant populations.
  • It's also interesting to note that if we expanded this to a world admixture analysis, beyond WHG+EEF+ANE, then there would likely be a strong correlation between WHG+EEF+ANE combined and Haplogroup I.
  • Haplogroup R1a's regression fit with ANE shows a good but apparently nonlinear correlation. This could indicate that beyond a certain threshold of ANE percentage, there tends to have been expansions of the R1a within those populations.
  • Haplogroup R1a actually shows a correlation with WHG as well. This is good evidence for the R1a expansion into Europe (Corded Ware etc.) picking up assimilated hunter-gatherers as it went along, but not picking up farmers so much.
  • I think that the average (WHG-I) and average (ANE-R1a) are significant. The fact that ave(WHG-I) is quite positive while ave(ANE-R1a) is slightly negative is strong evidence for population absorptions magnifying the Y-lines, but not the autosomal lines, of the absorbing population at the expense of the absorbed population.
 
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Heck, very interesting correlations and Y frequency trends. I think they nicely indicate that hgs of I (I think mainly I2a) interacted much sooner with EEF than R1a. With R1a located more North-East clinged to hunting and gathering for much longer.
However, the huge number of I2a-Dinaric in Balkans might be skewing the results. I mean influencing them too much towards EEF. Balkans was an epicenter of EEF, and if I2a moved there relatively recently it would have picked up unproportional (to most Is) amount of EEF.
Regardless, I think in general hg I experienced farming sooner than R1a.
  • Haplogroup I doesn't correlate with much of anything, with its strongest positive correlation being with WHG as we may expect, but even with that one, it is a weak correlation. This could be explained by the haplogroup being widespread in Europe early, but with several later expansions into non-WHG-dominant populations.
Exactly, unlike R1a.

  • Haplogroup R1a actually shows a correlation with WHG as well. This is good evidence for the R1a expansion into Europe (Corded Ware etc.) picking up assimilated hunter-gatherers as it went along, but not picking up farmers so much.
But if they stayed for thousands of years in vicinity (far east europe) then just before the time of Corded Ware it might have been mostly WHG already through autosomal component. Looking at the chart, anything population above 20% R1a shows WHG from 0.3-0.5 that's very consistent, and for highest concentration of R1a at 0.4. It might mean that R1a came with 40% of their own WHG.
R1a - WHG.JPG
  • I think that the average (WHG-I) and average (ANE-R1a) are significant. The fact that ave(WHG-I) is quite positive while ave(ANE-R1a) is slightly negative is strong evidence for population absorptions magnifying the Y-lines, but not the autosomal lines, of the absorbing population at the expense of the absorbed population.
I don't understand positive-negative "values" when describing these charts. Can you elaborate?

This is interesting too:
R1a-ANE.JPG
Above 0.1 (above the noise level?), for higher concentration of R1a the ANE component is very steady around 16%. I think it indicates one time mixture of R1a source population with ANE source, or (probably most likely wide spread event of ANE expansion over huge area of Eurasia.
I wish we could compare these with R1a reach area of Pakistan, Kurdistan, India.

Great job Sparkey
Thanks
 
Heck, very interesting correlations and Y frequency trends. I think they nicely indicate that hgs of I (I think mainly I2a) interacted much sooner with EEF than R1a. With R1a located more North-East clinged to hunting and gathering for much longer.

Interesting way of looking at it. It would indeed seem that different groups of I carriers took up farming at different times, and hence some expanded into EEF populations, then different groups expanded into ANE populations, then others waited until late to expand.

However, the huge number of I2a-Dinaric in Balkans might be skewing the results. I mean influencing them too much towards EEF. Balkans was an epicenter of EEF, and if I2a moved there relatively recently it would have picked up unproportional (to most Is) amount of EEF.
Regardless, I think in general hg I experienced farming sooner than R1a.

Northern I2a-Din probably contributed to the I/ANE affinity as well. If we took out late expansions (say post-Bronze Age), then I bet that the I/WHG correlation strengthens somewhat. But then there would still be the EEF-linked I2-M26 subclade and some others. Not to mention that I1 had a strongly anti-EEF expansion around the same time as the I2a-Din expansion, so it may be a wash because of that.

But if they stayed for thousands of years in vicinity (far east europe) then just before the time of Corded Ware it might have been mostly WHG already through autosomal component. Looking at the chart, anything population above 20% R1a shows WHG from 0.3-0.5 that's very consistent, and for highest concentration of R1a at 0.4. It might mean that R1a came with 40% of their own WHG.

It's tough to call this hypothesis at the moment. One piece of evidence against it would be that, if we suppose WHG's source population(s) to have been strongly I dominant as is normally suggested, then the diversity patterns of practically all known I subclades are inconsistent with it. I wouldn't discount an Eastern part-WHG non-I (or extinct-I) group, though, which makes this hypothesis plausible nonetheless.

I don't understand positive-negative "values" when describing these charts. Can you elaborate?

Sorry for the jargon. It's pretty simple:
  • (WHG-I) = percent WHG minus percent Haplogroup I
  • (ANE-R1a) = percent ANE minus percent R1a
  • average (WHG-I) = average (WHG-I) of all the sampled populations
  • average (ANE-R1a) = average (ANE-R1a) of all the sampled populations
I also took averages of the absolute values of (WHG-I) and (ANE-R1a) but I don't think those say much.

This is interesting too:
View attachment 6156
Above 0.1 (above the noise level?), for higher concentration of R1a the ANE component is very steady around 16%. I think it indicates one time mixture of R1a source population with ANE source, or (probably most likely wide spread event of ANE expansion over huge area of Eurasia.

I think this is a good analysis. The big vertical tower that stretches the R1a levels higher than their corresponding ANE frequencies could be post-R1a-migration-event founder effects. Looks like that tower is made up of Belorussians, Ukrainians, Lithuanians, and Czechs... perhaps a pan-Balto-Slavic founder effect reinforced by later local founder effects?
 
It's absolutely useless and unscientific analysis. You are trying to find correlation between autosomal data and y-dna haplos while in fact autosomal data of a person (some population) depends on much more factors (e.g. you should at least take into account as well mtDNA).
 
The (Y-DNA I, ANE) graph seems skewed by the single dot in the upper left corner. Without it it would much resemble the (Y-DNA R1a, ANE) graph I think.
The (Y-DNA R1a, ANE) graph would probably look smoother if R1b is incuded I guess.

I'm still a bit sceptic about correlating haplogroups with large autosomal components. It is much more reliable when applied to sparse, recent or exotic autosomals, like R1b-Gedrosian for example.
However, still interesting experiment.
 
It's tough to call this hypothesis at the moment. One piece of evidence against it would be that, if we suppose WHG's source population(s) to have been strongly I dominant as is normally suggested, then the diversity patterns of practically all known I subclades are inconsistent with it. I wouldn't discount an Eastern part-WHG non-I (or extinct-I) group, though, which makes this hypothesis plausible nonetheless.
I don't see a problem of WHG being wholly transferable from hg I giving the long timescale from LGM or at least all neolithic. Same way that blond hair was transferred from original population to Baltic area across many haplogroups and cultures. At the time of Bronze Age Corded Ware, WHG admixture could have been spread very far into eastern Europe infiltrating R1a.
It is still plausible that transfer happened later from Bronze Age till current times. From native population to R1a/Corded Ware newcomers. 5k years it is not such short time to make it impossible. I just think it is less likely though, because newcomers were farmers and as such they outnumbered local H-Gs 10 to 1. The WHG signal would have dropped to 10%, same as it happened in south Europe in presence of EEF.
I think Corded Ware period was the time when finally H-Gs of North-East became successful farmers, both R1a and I at the same time. That's why WHG admixture survived in substantial level.
Other reason why R1a already contained WHG is that otherwise they would have to contain only EEF+ANE before Corded Ware. I'm not sure how EEF could have gotten to R1a area circumventing WHGs?


I think this is a good analysis. The big vertical tower that stretches the R1a levels higher than their corresponding ANE frequencies could be post-R1a-migration-event founder effects. Looks like that tower is made up of Belorussians, Ukrainians, Lithuanians, and Czechs... perhaps a pan-Balto-Slavic founder effect reinforced by later local founder effects?
I looked at the table again and to my understanding ANE has to be very ancient all over the europe, so old that it transcends all the haplogroups. It is very evenly spread all over europe with slight gradient from east to west, and this denotes a very ancient event. It might be so ancient that EEF had ANE at 10% already before they arrived. Therefore EEF didn't change much of ANE level in south Europe. Eastern Europe is more elevated with ANE from later migrations of steppe tribes.
 
I looked at the table again and to my understanding ANE has to be very ancient all over the europe, so old that it transcends all the haplogroups. It is very evenly spread all over europe with slight gradient from east to west, and this denotes a very ancient event. It might be so ancient that EEF had ANE at 10% already before they arrived. Therefore EEF didn't change much of ANE level in south Europe. Eastern Europe is more elevated with ANE from later migrations of steppe tribes.

But the ANE/WHG ratio is much higher in western and southern europe than in north-eastern europe. And in southern europe, only Sardinia has practically 0% ANE and Basque also has very low ANE/WHG ratio, as both are non-IE peoples, which indicates a rather late distribution of ANE at least to west and parts of south europe. I agree only for north and east europe that ANE is very old, because Motala samples were already ANE.
In particular Scotland has almost the same absolute ANE score as Estonia where it peaks (0.182 vs. 0.183), but still has much less WHG than Estonia (0.428 vs. 0.495). Since I doubt that ANE is more ancient in Scotland than in Estonia (Loshbour had no ANE) I think it came later during Bronze age to Scotland. Maybe a part ANE was already there before, but it must have been minor.

(see 'Extended Data Table3' from the paper)
 
Eurogenes has recently come up with a three-component admixture analysis based on ancient samples, in which the three components are named WHG (West European Hunter-Gatherer), EEF (Early European Farmer), and ANE (Ancient North Eurasian). This analysis can be applied to existing European populations. See here.

Based on existing ancient samples and analysis of modern samples, there's a strong indication that Haplogroup I was important in the source population(s) of WHG, and Haplogroup R (perhaps especially R1a?) was important in the source population(s) of ANE. But do these patterns still hold? Taking the breakdown from Eurogenes and the Y-DNA frequencies from Eupedia, I get the following scatter plots and basic regression lines:

9esy.png


Furthermore, we can see some interesting patterns when looking at the difference between haplogroup and component frequency population-by-population:

wi9n.png


What to take from this? Here are some of my takes:

  • Haplogroup I doesn't correlate with much of anything, with its strongest positive correlation being with WHG as we may expect, but even with that one, it is a weak correlation. This could be explained by the haplogroup being widespread in Europe early, but with several later expansions into non-WHG-dominant populations.
  • It's also interesting to note that if we expanded this to a world admixture analysis, beyond WHG+EEF+ANE, then there would likely be a strong correlation between WHG+EEF+ANE combined and Haplogroup I.
  • Haplogroup R1a's regression fit with ANE shows a good but apparently nonlinear correlation. This could indicate that beyond a certain threshold of ANE percentage, there tends to have been expansions of the R1a within those populations.
  • Haplogroup R1a actually shows a correlation with WHG as well. This is good evidence for the R1a expansion into Europe (Corded Ware etc.) picking up assimilated hunter-gatherers as it went along, but not picking up farmers so much.
  • I think that the average (WHG-I) and average (ANE-R1a) are significant. The fact that ave(WHG-I) is quite positive while ave(ANE-R1a) is slightly negative is strong evidence for population absorptions magnifying the Y-lines, but not the autosomal lines, of the absorbing population at the expense of the absorbed population.
These are not the only haplogroups which exist in the tests. The tests are meant for no haplogroup specifically. Scholars state, the numbers that range close to:
EEF 70
WHG 20
ANE 10
are from the areas of North Portugal, Northern Spain, Southern france, Northern italy, the alpine areas of swiss, austrian and southern germany..............ending on the fringes of Hungaria

I am
EEF 69.20886831
WHG 20.20271451
ANE 10.58841718


I sit between Bergamo and South France ..................which is yours
 
...Same way that blond hair was transferred from original population to Baltic area across many haplogroups and cultures...

Surely you jest. Did you really think you could pass this conjecture off unchallenged?

On a larger note, I'm going to have to agree with El Horsto... the science linking haplogroup to autosomal in these samples seems flimsy to me at best.

And please allow me to go off on a related tangent here-- one must look no further than Youtube to see that autosomal readings (as they apply to phenotype) at this point are simply not that accurate. (I recently watched a video where the genetic test missed both eye color and hair texture from a poster who read his results on camera-- and this was from a living, breathing individual.)

**EDIT**
Youtube channel referenced above is called "Heisaswethink Heis" and the video is labelled "23 and me". Start watching at 4:39 to save time. Actually the test missed eye color, hair texture, and male pattern baldness factor (at least 3 out of 13 areas). Video can be found by searching for 23 and Me in youtube search engine.

I would think these tests would be far more accurate with "fresh" testing material vs. DNA that is hundreds/thousands of years old. What does this tell us about the validity of the readings from these ancient samples?
 
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But the ANE/WHG ratio is much higher in western and southern europe than in north-eastern europe. And in southern europe, only Sardinia has practically 0% ANE and Basque also has very low ANE/WHG ratio, as both are non-IE peoples, which indicates a rather late distribution of ANE at least to west and parts of south europe. I agree only for north and east europe that ANE is very old, because Motala samples were already ANE.
In particular Scotland has almost the same absolute ANE score as Estonia where it peaks (0.182 vs. 0.183), but still has much less WHG than Estonia (0.428 vs. 0.495). Since I doubt that ANE is more ancient in Scotland than in Estonia (Loshbour had no ANE) I think it came later during Bronze age to Scotland. Maybe a part ANE was already there before, but it must have been minor.

(see 'Extended Data Table3' from the paper)
ANE map.jpg
Looking at this quick map I made, one can argue that ANE was brought to Europe by waves of invasions from the east. However if ANE is ubiquitous and almost at same level in every person from same region that it has to be very old and had time to spread so evenly from 10 to 20 percent in every european. If it was Bronze Age recent you could see bigger disproportions between people of same country, and many people completely missing ANE. Same way you can find lactose intolerant people in central europe. So far we can't find even one person missing ANE component in Europe. It has got to be very ancient.
 
View attachment 6158
Looking at this quick map I made, one can argue that ANE was brought to Europe by waves of invasions from the east. However if ANE is ubiquitous and almost at same level in every person from same region that it has to be very old and had time to spread so evenly from 10 to 20 percent in every european. If it was Bronze Age recent you could see bigger disproportions between people of same country, and many people completely missing ANE. Same way you can find lactose intolerant people in central europe. So far we can't find even one person missing ANE component in Europe. It has got to be very ancient.

looking at your map....the magyars came from the urals........makes sense
 
View attachment 6158
Looking at this quick map I made, one can argue that ANE was brought to Europe by waves of invasions from the east. However if ANE is ubiquitous and almost at same level in every person from same region that it has to be very old and had time to spread so evenly from 10 to 20 percent in every european. If it was Bronze Age recent you could see bigger disproportions between people of same country, and many people completely missing ANE. Same way you can find lactose intolerant people in central europe. So far we can't find even one person missing ANE component in Europe. It has got to be very ancient.

Scotland is an outlier in the ANE component map and an outlier in SWG map. That is interesting. Do you also have a map for the other two components? If so, can you post them?
 
View attachment 6158
Looking at this quick map I made, one can argue that ANE was brought to Europe by waves of invasions from the east.
However if ANE is ubiquitous and almost at same level in every person from same region that it has to be very old and had time to spread so evenly from 10 to 20 percent in every european.

I don't think this is significant. R1b for instance also spread quite evenly across large parts of Europe and still it happened recently.

If it was Bronze Age recent you could see bigger disproportions between people of same country, and many people completely missing ANE. Same way you can find lactose intolerant people in central europe. So far we can't find even one person missing ANE component in Europe. It has got to be very ancient.

Well, Sardinia has no ANE but it has WHG instead. Loschbour in Luxembourg had no ANE and was fully WHG. For me this is enough evidence to assume a rather late ANE dispersal to west and south. The higher ANE/WHG > 1 ratio elsewhere in southern europe can be explained by bronze age invaders, because these places 'coincidentally' are accompanied by late haplogroups like R1b and R1a for instance and speak indo-european languages. I'm correlating haplogroups here because ANE is rare in these places and R1b is recent, which makes it more significant.

Also your map shows the absolute ANE levels only, not the ANE/WHG ratio. I agree that WHG would show almost the same east-west gradient as ANE, but that's why I think the ANE/WHG ratio is so important and because of the overlap of both in NE europe.
 
View attachment 6158
Looking at this quick map I made, one can argue that ANE was brought to Europe by waves of invasions from the east. However if ANE is ubiquitous and almost at same level in every person from same region that it has to be very old and had time to spread so evenly from 10 to 20 percent in every european. If it was Bronze Age recent you could see bigger disproportions between people of same country, and many people completely missing ANE. Same way you can find lactose intolerant people in central europe. So far we can't find even one person missing ANE component in Europe. It has got to be very ancient.

I could agree partially because of another reason, which is that WHG and ANE are probably very similar or just two ends within the same paleolithic component, because, if I understood correctly, the authors just defined WHG = Loschbour.
 
It's absolutely useless and unscientific analysis. You are trying to find correlation between autosomal data and y-dna haplos while in fact autosomal data of a person (some population) depends on much more factors (e.g. you should at least take into account as well mtDNA).

You're missing the point. I don't dispute that autosomal DNA depends on more than Y-DNA haplogroups. This is just a visualization of how well certain haplogroups correlate with certain autosomal components, with an open possibility that they may not correlate at all, or even that data may be contradictory/insufficient. It's not an attempt to break an autosomal component down into its haplogroups or anything like that.
 
I don't think this is significant. R1b for instance also spread quite evenly across large parts of Europe and still it happened recently.



Well, Sardinia has no ANE but it has WHG instead. Loschbour in Luxembourg had no ANE and was fully WHG. For me this is enough evidence to assume a rather late ANE dispersal to west and south. The higher ANE/WHG > 1 ratio elsewhere in southern europe can be explained by bronze age invaders, because these places 'coincidentally' are accompanied by late haplogroups like R1b and R1a for instance and speak indo-european languages. I'm correlating haplogroups here because ANE is rare in these places and R1b is recent, which makes it more significant.

Also your map shows the absolute ANE levels only, not the ANE/WHG ratio. I agree that WHG would show almost the same east-west gradient as ANE, but that's why I think the ANE/WHG ratio is so important and because of the overlap of both in NE europe.

I agree that a good portion of ANE must have arrived in Europe relatively late, with the exception of some inflow into the northeast by the Mesolithic (Motala) and with historical era migrations as well, as the authors of Lazaridis et al point out.

I suppose everything is in the eye of the beholder...I see a definite east west and particularly north-east/south-west cline. I think the north east can be partially explained by my comment above. It wasn't, however, in western Europe in the late Mesolithic, going by Louschbar.

Spain and southern France are relatively light in it, and so are parts of Italy. It looks to me as if there was another gene flow starting somewhere around the Caucasus/Iran, and petering out by the time it got to central Europe.

I also wonder whether R1b is indeed the primary carrier of these Indo-European languages. Believe me, I know that's the orthodoxy on this Board, but there are some facts that don't quite fit and perhaps might argue for an R1a role in western Europe as well. For instance, if I am reading the map correctly, the ANE light areas in Italy include part of the Etruscan speaking areas, and perhaps the Raetian speaking areas? Or is that half moon area too far west for that? (I know that on the eastern part of the Alps there was some R1a geneflow, but not in the western part of the Alps.) Certainly the Basque speaking area is extremely light in it as well. Btw, these areas-Tuscany, northern Italy, and the Basque region-are very high in R1b, but did not adopt Indo European languages until very late. I'm not sure about the Basques, but there's very little R1a in those regions of Italy.

I also wonder how this fits with not only R1b spreading this component in Europe, but also how, even accepting that premise, it fits with the standard model of Indo-European bearing R1b having a staging ground in the Alps. You would think from that, that the northern areas of Italy would have a lot of ANE if R1b was the primary carrier.

Southern Italy presents another issue. There's much less R1b there, and what there is of it is heavily of the eastern variety, lots of J2a, but also quite a bit of R1a, and it has the most ANE of any area in Italy. Is that just because there is less WHG to "divide up the pie", or is it the result of Bronze Age incursions from Greece(the elite Myceneans were R1a weren't they) and perhaps the Caucasus/Iran by way of Greece carrying R1a and J2.

Just my two cents.
 
I agree that a good portion of ANE must have arrived in Europe relatively late, with the exception of some inflow into the northeast by the Mesolithic (Motala) and with historical era migrations as well, as the authors of Lazaridis et al point out.

I suppose everything is in the eye of the beholder...I see a definite east west and particularly north-east/south-west cline. I think the north east can be partially explained by my comment above. It wasn't, however, in western Europe in the late Mesolithic, going by Louschbar.

Spain and southern France are relatively light in it, and so are parts of Italy. It looks to me as if there was another gene flow starting somewhere around the Caucasus/Iran, and petering out by the time it got to central Europe.

I also wonder whether R1b is indeed the primary carrier of these Indo-European languages. Believe me, I know that's the orthodoxy on this Board, but there are some facts that don't quite fit and perhaps might argue for an R1a role in western Europe as well. For instance, if I am reading the map correctly, the ANE light areas in Italy include part of the Etruscan speaking areas, and perhaps the Raetian speaking areas? Or is that half moon area too far west for that? (I know that on the eastern part of the Alps there was some R1a geneflow, but not in the western part of the Alps.) Certainly the Basque speaking area is extremely light in it as well. Btw, these areas-Tuscany, northern Italy, and the Basque region-are very high in R1b, but did not adopt Indo European languages until very late. I'm not sure about the Basques, but there's very little R1a in those regions of Italy.

I also wonder how this fits with not only R1b spreading this component in Europe, but also how, even accepting that premise, it fits with the standard model of Indo-European bearing R1b having a staging ground in the Alps. You would think from that, that the northern areas of Italy would have a lot of ANE if R1b was the primary carrier.

Southern Italy presents another issue. There's much less R1b there, and what there is of it is heavily of the eastern variety, lots of J2a, but also quite a bit of R1a, and it has the most ANE of any area in Italy. Is that just because there is less WHG to "divide up the pie", or is it the result of Bronze Age incursions from Greece(the elite Myceneans were R1a weren't they) and perhaps the Caucasus/Iran by way of Greece carrying R1a and J2.

Just my two cents.

The half moon area is noted as the early gallic "invasion" of northern Italy. It does sit in the "western Raeti" area ....now known as Romansch linguistic zone
 
The (Y-DNA I, ANE) graph seems skewed by the single dot in the upper left corner. Without it it would much resemble the (Y-DNA R1a, ANE) graph I think.
...........

Can you address this, sparky? If the results for I resembled those for R1a with respect to ANE, I think that would require different conclusions than one where the results for I seem fairly flat in all three graphs.
 
I agree that a good portion of ANE must have arrived in Europe relatively late, with the exception of some inflow into the northeast by the Mesolithic (Motala) and with historical era migrations as well, as the authors of Lazaridis et al point out.

I suppose everything is in the eye of the beholder...I see a definite east west and particularly north-east/south-west cline. I think the north east can be partially explained by my comment above. It wasn't, however, in western Europe in the late Mesolithic, going by Louschbar.

Spain and southern France are relatively light in it, and so are parts of Italy. It looks to me as if there was another gene flow starting somewhere around the Caucasus/Iran, and petering out by the time it got to central Europe.

I also wonder whether R1b is indeed the primary carrier of these Indo-European languages. Believe me, I know that's the orthodoxy on this Board, but there are some facts that don't quite fit and perhaps might argue for an R1a role in western Europe as well. For instance, if I am reading the map correctly, the ANE light areas in Italy include part of the Etruscan speaking areas, and perhaps the Raetian speaking areas? Or is that half moon area too far west for that? (I know that on the eastern part of the Alps there was some R1a geneflow, but not in the western part of the Alps.) Certainly the Basque speaking area is extremely light in it as well. Btw, these areas-Tuscany, northern Italy, and the Basque region-are very high in R1b, but did not adopt Indo European languages until very late. I'm not sure about the Basques, but there's very little R1a in those regions of Italy.

I also wonder how this fits with not only R1b spreading this component in Europe, but also how, even accepting that premise, it fits with the standard model of Indo-European bearing R1b having a staging ground in the Alps. You would think from that, that the northern areas of Italy would have a lot of ANE if R1b was the primary carrier.

Southern Italy presents another issue. There's much less R1b there, and what there is of it is heavily of the eastern variety, lots of J2a, but also quite a bit of R1a, and it has the most ANE of any area in Italy. Is that just because there is less WHG to "divide up the pie", or is it the result of Bronze Age incursions from Greece(the elite Myceneans were R1a weren't they) and perhaps the Caucasus/Iran by way of Greece carrying R1a and J2.

Just my two cents.

I agree. The haplo-autosomal matching possibly again shows its limits even for R1b-ANE. After all it all could be even a false positive, but rather unlikely at the moment. The authors mention a sudden mtDNA change in Central europe during Bronze-age to be indicative for the time of ANE distribution. Looking at single Y-HG or mtDNA-HG alone is certainly risky, but it fits so nicely with the IE theory here that it is tempting to make the bet at the moment. And if it does not fit exactly for some regions it always can be easily explained away by HG-drift, you know. That being said, Y-HG R1b history is by no means 100% certainly IE for me as well.

The north-east/south-west cline you mention is obviously strong for ANE, but so it is also for WHG. But my point is that the ANE/(ANE+WHG) ratio for instance is higher in Scotland, France, Orkney and most southern Europe than in Belarus,Ukraine and Estonia, despite ANE has a more eastern ancestry than WHG.
 
Scotlands relative high ANE admixture combined with a relative high WHG admixture makes it an interesting place. The British isles were in contact with the mainland as recent as 10.000 years ago. Recently a map has been produced of so called Doggerland, the name of the middle North Sea area that was above sea level then.

http://www.nature.com/news/2008/080709/full/454151a.html?s=news_rss

In the North Sea mesolithic finds are found by fisherman, as that article states. North Scotland could have been a refuge of these people, like the Baltic.
 

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