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Author Topic: Different genetic perspectives on human history in Europe and the Caucasus  (Read 10490 times)
JeanL
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« on: May 30, 2012, 01:27:08 AM »

Appears to be a nice summary of all the data up until April, 2012 concerning haplogroups in Europe and the Caucasus, touches everything from Balaresque.et.al.2010 to Myres.et.al.2010, to Busby.et.al.2012.

Different genetic perspectives on human history in Europe and the Caucasus: the stories told by uniparental and autosomal markers

Quote from: Mari Järve

Conclusions

  • The mutation M458, representing a founder effect around the Mesolithic/Neolithic transition in Central and East Europe, separates most of the European R1a carriers from the spread of this Y chromosome haplogroup that spans from South Asia to Siberia and Europe.
  • In West Europe another major Holecene era founder effect is denoted by the mutation M412 within the Y chromosome haplogroup R1b, and the spatial and temporal pattern of a sub-clade within R1b-M412 is in close correlation with the spread of the Linear Pottery Neolithic culture.
  • Populations of the Caucasus are autosomally much more uniform than might be expected from their diverse linguistic and ethnic backgrounds. Conversely, the variation of Caucasian Y chromosome lineages exhibits sharp differences between populations and sub regions, likely due to founder effects and genetic drift in (patrilineally) isolated populations.
  • The Caucasus has not served as a corridor for the movement of people from Near/Middle East to East Europe or to Europe in general. Instead, there is a genetic continuity from the Near Eastern to East European populations along the western coast of the Black Sea, suggesting a predominant trajectory of the flow of genes and humans.
  • Y chromosome STRS with longer repeat units have a lower rate of evolution, in some cases making them better suited for population genetic studies than their counterparts with shorter repeat units.

Also from the same author, and apparently the source of most of Myres.et.al.2010 data:

Refining the phylogeny and phylogeography of the human Y chromosome haplogroup R1b1b
« Last Edit: May 30, 2012, 01:30:10 AM by JeanL » Logged
Maliclavelli
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« Reply #1 on: May 30, 2012, 02:16:10 AM »

From this paper it is clear that R-L23 had some centres of diffusion, independent, and that the Alpine zone was one of this and from that L23 came all the European subclades. I consider victorious my battle (actually it has been a war) about the Italian Refugium. Call it Alpine if you want, but I consider my war finished, and, if you permit, with a complete victory.

Maliclavelli is: Prof. Gioiello Tognoni (Calcinaia, Pisa, Italy: 5 March 1948), R-L23+, K1a1b1e.

« Last Edit: May 30, 2012, 02:20:45 AM by Maliclavelli » Logged

Maliclavelli


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palamede
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« Reply #2 on: May 30, 2012, 06:04:39 AM »

Appears to be a nice summary of all the data up until April, 2012 concerning haplogroups in Europe and the Caucasus, touches everything from Balaresque.et.al.2010 to Myres.et.al.2010, to Busby.et.al.2012.

Different genetic perspectives on human history in Europe and the Caucasus: the stories told by uniparental and autosomal markers

Quote from: Mari Järve

Conclusions

  • The mutation M458, representing a founder effect around the Mesolithic/Neolithic transition in Central and East Europe, separates most of the European R1a carriers from the spread of this Y chromosome haplogroup that spans from South Asia to Siberia and Europe.
  • In West Europe another major Holecene era founder effect is denoted by the mutation M412 within the Y chromosome haplogroup R1b, and the spatial and temporal pattern of a sub-clade within R1b-M412 is in close correlation with the spread of the Linear Pottery Neolithic culture.
  • Populations of the Caucasus are autosomally much more uniform than might be expected from their diverse linguistic and ethnic backgrounds. Conversely, the variation of Caucasian Y chromosome lineages exhibits sharp differences between populations and sub regions, likely due to founder effects and genetic drift in (patrilineally) isolated populations.
  • The Caucasus has not served as a corridor for the movement of people from Near/Middle East to East Europe or to Europe in general. Instead, there is a genetic continuity from the Near Eastern to East European populations along the western coast of the Black Sea, suggesting a predominant trajectory of the flow of genes and humans.
  • Y chromosome STRS with longer repeat units have a lower rate of evolution, in some cases making them better suited for population genetic studies than their counterparts with shorter repeat units.

Also from the same author, and apparently the source of most of Myres.et.al.2010 data:

Refining the phylogeny and phylogeography of the human Y chromosome haplogroup R1b1b
The papers are from a researcher of Tartu University-Estonia
Interesting like synthesis of studies, but according to the knowledge of SNPs in 2008. Now, in Europe, in more of the R1a1a1g1-M458 branch (Central Europe, peak in Central,South Poland), Bohemia), 3 important branches have been found : R1a1a1i-L664 (Germanic), R1a1a1g1-Z280 (Eastern and central Europe), R1a1a1g3 (Western and North Europe). Asiatic R1a is dominated  by the big branch R1a1a1h-Z93.  

Conclusions of the other paper :
"R1b1b" = R1b1a-P297
"R1b1b1" = R1b1a1-P73
"R1b1b2" = R1b1a2-M269
M412 = R1a1a2a1-L11
M466 = R1a1a2a1a1b3-U152
Quote from: Mari Järve

1. The two main sub-hgs of the Y chromosome hg R1b1b, R1b1b1 and R1b1b2, differ
in age and geographic distribution:
• R1b1b1 is a rare and older lineage (coalescence age 27,233±13,060 years),
found at low to moderate frequencies among Eastern European, Turkic and
Caucasian samples, being totally absent in Western Europe;
• R1b1b2 is considerably younger (coalescence age 18,301±3,566 years) and
common in Western Europe, but also spread in some of the Bashkir populations;
2. The two-partite spread of sub-hg R1b1b2  is mostly explained by the novel SNP
marker M412, which has its ancestral state in the majority of the eastern R1b1b2
samples (the R-M269* lineage), and its derived state in the absolute majority of the
western R1b1b2 samples (the R-M412 lineage and its sub-lineages);
3. The sole notable exception to the western spread of the R-M412 lineage, the
northern Bashkirs, who exhibit an uncommonly high frequency of sub-hg R-M466
(inside the R-M412 lineage), appears to be the result of a strong founder effect, as
these samples also have nearly identical STR haplotypes;
4. The M412 mutation has a likely Western European origin, possibly being a marker
of the recolonisation from an isolated population nucleus in the Iberian peninsula
after the LGM 13-20 kya (Semino et al. 2000);
5. Recalibrating the effective mutation rate of STR markers of 6.9·10-4  per 25 years
(Zhivotovsky et al. 2004) based on the variances of 15 markers of the Applied
Biosystems AmpFlSTR® Yfiler™ Kit had very little effect, but the calculations
suggested that the mutation rate of penta- and hexanucleotide STR markers is
significantly lower, estimated as 2.4·10-4 per 25 years;
6. As illustrated by an analysis of  of the STR haplotypes of sister clades R1b1b and R1a, STR markers, including penta- and hexanucleotide microsatellites, can be used to distinguish Y chromosome hgs and, in some cases, subdivisions within hgs, without the help of SNP marker data.
For 5 and 6, I suppose these results are also found in different tables of mutation rate for each STR. This can be linKed  to a lot of workS and discussions about the validity to calculate dates by the divergence of STRs
For 4, the author Mari Järve refers to the paleolithic western origin of R1b-M412/L11 and its sub-branches. Very controversial by fans of neolitic/chalcolitic oriental origins. Personally, although no present scientifiv proof supports it, I guess R1b came to western europe with Gravettians from South Siberia (35,000BP), our Esthonian author thinks Gravettian was the culture of Hg I coming from Near East. I guess hg I came from Middle East/Zagros (45,000bp)with the Proto-Aurignacian derived from Zagros Baradostian.  

For 1,2,3, Bashkirs are a very interesting population. Maybe, indicating the origin of R1b : peak of R1b1a1-M73 in South-East Oural ; presence of "old" branches  R1b=M269, R1b-L23, R1b-L11 isolated in this region of Eurasia. But presence of new  branchd R1b-U152 in  North Oural  with haplotype divergence showing  a recent founding effect is troubling.  Bashkir U152/M466 exists in a small Bashkir trinbe in Perm Krai in Central-West Oural.
« Last Edit: May 30, 2012, 10:59:56 AM by palamede » Logged

Y=G2a3b1a2-L497 Wallony-Charleroi; Mt=H2a2a1 Normandy-Bray
Dodecad-DiY: E Eur 9,25% W Eur 48,48% Med 28,46% W Asia 11,70%
World9: Atl-Balt 67,61% Southern 13,23% Cauc-Gedr 12,73%
K12a: North-E 39,71% Med 37,9% Cauc 12,55% Gedr 5,78% SW Asia 2,13%
ironroad41
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« Reply #3 on: May 30, 2012, 07:50:31 AM »

Nice find Jean L.!  This is a lot to chew on.  It does support most of Busbys work and Zhivs analysis.  It will be very interesting to read the comments on this work by the "amateur genetic community".  Its apparent already that Machiavelli is ecstatic.

I'll have to read in more detail his comments about longer STR motifs and their applicability to TMRCA estimates, but off the top, I'm sure he can't mean CDY a,b.

My overall impression is very positive, at least it supports most of my points of view. Based on this work, maybe we should rethink R1b again?
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Maliclavelli
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« Reply #4 on: May 30, 2012, 08:36:24 AM »

Its apparent already that Machiavelli is ecstatic.
After having read the paper, I should say that it doesn't say anything new, only a review of previous studies we did already know and discussed.
Important for me was the map of L23, which demonstrates, I think, what for me is the Italian (or Alpine) Refugium I lay at least at the Younger Dryas time.
That L23 is more Northwards doesn't exclude that during the Younger Dryas was more Southwards, but for me nothing changes.
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Maliclavelli


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Richard Rocca
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« Reply #5 on: May 30, 2012, 08:47:39 AM »

The map of U106 (aka M405) is completely wrong. A peak in NW Switzerland with decreasing frequency towards the lower Rhine goes against all known studies, including Myres.
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Maternal: H
JeanL
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« Reply #6 on: May 30, 2012, 08:50:10 AM »


The papers are from a researcher of Tartu University-Estonia
Interesting like synthesis of studies, but according to the knowledge of SNPs in 2008.

Well the paper you are quoting, which is the second one I posted, is indeed from 2008, hence the old nomenclature.

http://www.ebc.ee/kaitsmised/2008/kaitsmisele_tulevad_3_2_magistritood/Mari_Jarve_MSc_thesis.pdf
That was his MSc’s thesis, and in fact it includes most of the data used by Myres.et.al.2010, which should be no surprised given that his/her mentors are coauthors on the Myres.et.al.2010, and Rootsi is the main author of Rootsi.et.al.2012.  


Conclusions of the other paper :
"R1b1b" = R1b1a-P297
"R1b1b1" = R1b1a1=P73
"R1b1b2" = R1b1a2-M269
M412 = R1a1a2a1-L11
M466 = R1a1a2a1a1a-U106

Here is figure-9 from the MSc Thesis, and it shows the phylogenetic tree of R1b as of 2008.

http://i1133.photobucket.com/albums/m582/jeanlohizun/Jarveetal2008Figure-9.jpg

As you can see “R1b1b1” is actually R1b-M73, I believe you have a typo in there, also R1b-M466 is R1b-U152, R1b-M405 is in fact R1b-U106, so Bashkirs do not have R1b-U106, they have R1b-U152, which was later known through the Myres.et.al.2010 study, due to the fact that is the same data.
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Maliclavelli
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« Reply #7 on: May 30, 2012, 08:53:34 AM »

Of course Western Tuscany is a little place and not representative, but what should I think?
I have tested 4 persons:

25% R-M269/DYS462=12
50% R-L23/L150+ (and of course I don’t count my son)
25% R (probably U152/DYS492=14, tested by SMGF)
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Maliclavelli


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JeanL
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« Reply #8 on: May 30, 2012, 08:54:54 AM »

The map of U106 (aka M405) is completely wrong. A peak in NW Switzerland with decreasing frequency towards the lower Rhine goes against all known studies, including Myres.

I believe there is a typo, or something, I too was baffled by it.  Anyhow, I wanted to concentrate on the latest PhD Thesis, I included the MSc Thesis as a side thing. 
I think it’s good to have it as a summary of everything up until April, 2012. It talks about the aDNA findings, and the Caucasus studies. Also find it interesting that they conclude that:

Y chromosome STRS with longer repeat units have a lower rate of evolution, in some cases making them better suited for population genetic studies than their counterparts with shorter repeat units.

Which is something I have been pondering about for a while.
« Last Edit: May 30, 2012, 08:55:17 AM by JeanL » Logged
rms2
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« Reply #9 on: May 30, 2012, 09:26:13 AM »

Obviously, the assumptions one starts with make all the difference. If one uses mutation rates that make R1b old enough to be Paleolithic in Europe, then - voila! - it is Paleolithic in Europe. If one does not, then it is not and must have come from someplace else at a later date.

The biggest part of the problem is no one knows for sure, and there is no consensus on Zhivotovsky versus germ line, etc. Y-dna itself has no certain way of telling us its age. When we find it in ancient remains, then we know for certain that it was in a certain place at a certain time.

Meanwhile, the Paleolithic thing, which I personally think is preposterous, staggers on like some sort of Caribbean zombie, and all the soporific arguments about this STR and that are next to meaningless.

"Paleolithic R1b" didn't have much of a following here until dna-forums died and we inherited some of its ex-members. I had kind of begun to think that no one believed that stuff anymore. Apparently, I was wrong.

Let's see if I can summarize it.

R1b-M269 arises in Asia in the distant Paleolithic past. Some of its carriers leave all their closest genetic cousins in the old homeland and trek across Europe or perhaps North Africa to arrive in Iberia in time to hole up there for the LGM. At some point this now-western R-M269 becomes mostly R-M412/L51. When it emerges from its LGM hibernation, it spreads eastward and northward into the rest of Europe in that form.

When the Neolithic Revolution occurs, R-M412 initially heads for the hills and tries to avoid the bearers of the strange new technology. Later, carriers of R-M412 learn how to farm and raise livestock and somehow out-reproduce the original Neolithic farmers. They eventually defy all the odds and become the dominant y haplogroup in most of Europe.

At one or more points during the lengthy European saga of R-M412, most of its bearers die off, leaving only a handful of males or perhaps just one male to transmit it to later generations. These "genetic bottlenecks" create the "illusion" of reduced age for western R-M412, but, rest assured, it really is of the greatest antiquity there.

Meanwhile, back in old Asia, the R-M269 xL51 stuff is still around, separated from its distant western cousins now by about 12k years.

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« Reply #10 on: May 30, 2012, 09:28:07 AM »

The thesis paper also states that R1b1b1 is absent among west Europeans. This isn't true at all as there is a cluster which contains an Italian, Spaniard, French/German and more- though I expect this is the result of their extremely limited dataset.

I also didn't know this R1b1b1 haplotype existed in the Caucasus among Balkars, it is currently absent from all the FTDNA R1b1b1 data - and seems to fall outside the 3 clusters Vineviz identified A, B1, B2:

13, 22, 14, 11, 14, 14/15, ........13,13,29
« Last Edit: May 30, 2012, 09:39:47 AM by A_Wode » Logged
Maliclavelli
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« Reply #11 on: May 30, 2012, 09:52:59 AM »

The thesis paper also states that R1b1b1 is absent among west Europeans. This isn't true at all as there is a cluster which contains an Italian, Spaniard, French/German and more- though I expect this is the result of their extremely limited dataset.

I also didn't know this R1b1b1 haplotype existed in the Caucasus among Balkars, it is currently absent from all the FTDNA R1b1b1 data - and seems to fall outside the 3 clusters Vineviz identified A, B1, B2:

13, 22, 14, 11, 14, 14/15, ........13,13,29
I have written a lot (also here) about R-M73 in Western Europe and I think having demonstrated that our haplotypes are more varied than the Asian ones, like also for R-M335.
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Maliclavelli


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JeanL
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« Reply #12 on: May 30, 2012, 09:55:13 AM »

Obviously, the assumptions one starts with make all the difference. If one uses mutation rates that make R1b old enough to be Paleolithic in Europe, then - voila! - it is Paleolithic in Europe. If one does not, then it is not and must have come from someplace else at a later date.

The biggest part of the problem is no one knows for sure, and there is no consensus on Zhivotovsky versus germ line, etc. Y-dna itself has no certain way of telling us its age. When we find it in ancient remains, then we know for certain that it was in a certain place at a certain time.

Meanwhile, the Paleolithic thing, which I personally think is preposterous, staggers on like some sort of Caribbean zombie, and all the soporific arguments about this STR and that are next to meaningless.

"Paleolithic R1b" didn't have much of a following here until dna-forums died and we inherited some of its ex-members. I had kind of begun to think that no one believed that stuff anymore. Apparently, I was wrong.

I didn’t bring this study as a “Paleolithic R1b” zombie, or whatever you wanna call it. Isn’t a bit of an Ad Hominem to compare a given theory to a Zombie? Nonetheless, the initial purpose of this was to have a summary of all studies published(including aDNA and Caucasus studies) up until April 2012. In fact in section 2.7 the author does an extensive analysis of the calculations of TMRCA, here are some excerpts:

Quote from: Mari.et.al.2012
The ‘evolutionary’ mutation rate, and even the use of Y-STRs for dating purposes in general, have also been heavily criticised. The main shortcoming of the ‘evolutionary’ rate is that it tends to overestimate dates. This is mostly due to men having different numbers of offspring, with the majority of men alive today descending from a relatively small percentage of forefathers (likely of higher social status). Therefore, a small number of more prolific forefathers have contributed the largest share of the accumulated Y-STR variance, which in its turn means that the variance is higher among the descendants of the prolific men than among the descendants of the less prolific men. Given this expansion of a few lineages at the expense of others and the fact that the more numerous descendants of the prolific forefathers are most likely to be sampled, we overestimate the time to the MRCA by mostly sampling men from lineages where Y-STR variance accumulates faster than the ‘evolutionary’ rate. The authors of the ASD method themselves have pointed out that an effective mutation rate higher than the ‘evolutionary’ rate would be observed in case of a sudden jump in the size of the haplogroup after its appearance or in case of an expanding population (Zhivotovsky et al. 2006), both of which are often reasonable assumptions for post-Neolithic human populations. The confidence intervals of Y-STR-based age estimates are wide, influenced by the chosen generation length, the inherent stochasticity of the  mutation process, and the mutation rate, which in its turn is influenced by the demographic history of a
particular haplogroup in a particular population (Zhivotovsky et al. 2006).

[…]

Until new and hopefully more reliable methods can be implemented, based for instance on SNPs from massive resequencing of a considerable portion (e.g., some tens of millions of bp) of the NRY combined with reliably dated calibration (derived, e.g., from ancient DNA studies), Y-STR variation analysis, despite its known imperfections, will continue to be used for dating. It is also likely that the new re-sequencing-based methods will offer, first and foremost, more precise estimates to date the major splits of the Y chromosome tree, whereas in case of the younger branches, the faster Y-STR clock may long remain the method of choice.

So the moral of the story, is hold you guns, and read the study before criticizing it of using erroneous assumptions.

Let's see if I can summarize it.

R1b-M269 arises in Asia in the distant Paleolithic past. Some of its carriers leave all their closest genetic cousins in the old homeland and trek across Europe or perhaps North Africa to arrive in Iberia in time to hole up there for the LGM. At some point this now-western R-M269 becomes mostly R-M412/L51. When it emerges from its LGM hibernation, it spreads eastward and northward into the rest of Europe in that form.

Not likely Asia, but somewhere in Western Russia/Ukraine, and likely it did so around 15-20 kya, so not so distant. In my opinion R1b-M269 was widespread in Europe, it wasn’t just holed up in Iberia, so no point to bring in the FC refuge.


When the Neolithic Revolution occurs, R-M412 initially heads for the hills and tries to avoid the bearers of the strange new technology. Later, carriers of R-M412 learn how to farm and raise livestock and somehow out-reproduce the original Neolithic farmers. They eventually defy all the odds and become the dominant y haplogroup in most of Europe.

It is likely that when the farmers first arrived to the Balkans they pushed some R1b-L23 folks Northeastwards, and hence why Romania gets a high variance. As for R1b-L51, I don’t think it existed yet, it probably emerged later on while hiding in Western Europe, the same would apply to R1b-L11, in fact neither one of those two experienced a sudden expansion, so it is likely they originated in a very small population that wasn’t that successful. As for out-reproducing the farmers, did the hunter-gatherers in the Steppe’s learn the technology from the farmers, and then conquered all of Europe. What is wrong with some of those folks that have been sitting around in Central Europe for a while learning the technology from the incoming invaders. Are hunter gatherers in Western Europe somehow dumber than those in the Steppe, such that the former can learn anything from the farmers, yet the latter manage to conquer all of Europe.

At one or more points during the lengthy European saga of R-M412, most of its bearers die off, leaving only a handful of males or perhaps just one male to transmit it to later generations. These "genetic bottlenecks" create the "illusion" of reduced age for western R-M412, but, rest assured, it really is of the greatest antiquity there.

Meh, R-M412 is neither part of a lengthy European saga, nor did it have a lot of bearers, so no need to think of a lot of them dying off, the big guys here are R1b-P312, they are the ones that took off abruptly.

Meanwhile, back in old Asia, the R-M269 xL51 stuff is still around, separated from its distant western cousins now by about 12k years.

Yes meanwhile, the R1b-L23(xL51) folks that were displaced towards the Steppes by the incoming farmers become the half story of the PIE group, the other half being R1a, and they go everywhere, but apparently just as they stop abruptly in Iran-Pakistan, they do so too around Central Europe, however the fact that some R1b-L23(xL51) is still found today in Western European shows that some of them did mingle around their distant cousins, and voila that explains why some R1b-P312 bearers are nonIndoEuropean speakers, whereas others aren't. If the R1b-L23(xL51) taught PIE to their cousins in Central Europe, then you get Celtic-Italic, you name it, expansions to explain the presence of IE languages in Western Europe. Whereas if R1b-L51 is born of PIE speaker R1b-L23 coming from the steppes in the Bronze age we would have a hard time explaining why groups with 80%+ of R1b-L51+ speak a nonIndoEuropean language.
« Last Edit: May 30, 2012, 10:02:50 AM by JeanL » Logged
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« Reply #13 on: May 30, 2012, 10:29:35 AM »

Just a point on language replacement/expansion. I have seen repeatedly the expression R1a taught IE to R1b or similar. That is rsented by some, as if R1b were some poor aboriginal population  taught by lofty R1a conquerors.
Languages expand usually, and more so in premodern times, by learning, not teaching. That is usually the case when an egalitarian, excluyent society meets a hierarchical, including society, so that members of the former join the later in order to move up the social ladder. That is a well known phenomenon described by sociologist Fredrik Barth and in fact it is the explanation adopted by Mallory to explain the expansion of IE languages into Western Europe.
« Last Edit: May 30, 2012, 10:30:05 AM by IALEM » Logged

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« Reply #14 on: May 30, 2012, 10:34:31 AM »

... My overall impression is very positive, at least it supports most of my points of view....
Maybe it is just me, but I think the assessment of the paper should be on the evidence, the analysis and the logic.  Whether it agrees with one point of view hopefully is not a big deal. We just want to get the best hypothesis of what happened and if this paper helps us understand that, it is good.  I'm glad for the additional focus on R1b.
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« Reply #15 on: May 30, 2012, 10:50:54 AM »

Just a point on language replacement/expansion. I have seen repeatedly the expression R1a taught IE to R1b or similar. That is rsented by some, as if R1b were some poor aboriginal population  taught by lofty R1a conquerors.
Languages expand usually, and more so in premodern times, by learning, not teaching. That is usually the case when an egalitarian, excluyent society meets a hierarchical, including society, so that members of the former join the later in order to move up the social ladder. That is a well known phenomenon described by sociologist Fredrik Barth and in fact it is the explanation adopted by Mallory to explain the expansion of IE languages into Western Europe.
I think some people may be mistaken in understanding negative feedback on the concept of R1a teaching R1b a language. I personally don't care if this was more demand-pull or force-push.

For example, I speak English. I am proud of that and would not have it any other way. I'm pretty sure, though, that some major lineages of mine spoke Slavic, other forms of German as well as Celtic languages. My paternal lineage probably spoke Celtic for a long period of time.  So what? It is a good thing to speak English today, I think.

I have some ancestors that hated Oliver Cromwell related to his work in Ireland, but on another side I may be related to him. So what? Should I resent myself? Should I resent my Slavic side which has R1a?  Of course, not. In reality, rather than being consider lofty, my R1a sides were poor farmers and actually given somewhat degradatory/humorous labels. I won't name them so I don't offend others even if they don't offend me. Such things are not offensive to me as I am a composite of both the offended and the offender.

However, I do argue against hypotheses that either appear wrong to me or that I can't understand. I do this to test them and see if their proponents have convincing arguments. I really do not know what the first haplogroup(s) who spoke PIE was. I do not know which haplogroup(s) spoke primary pre-PIE language(s). I don't see how we will ever know given they weren't putting this stuff in writing back then.

To say R1a taught R1b or that R1b learned IE languages from R1a is possible, but seems a bit simplistic of a view and I just plain don't see much direct evidence for it.  I guess we could argue about cirmcumstancial evidence, which we do, but there is a lot of cirmcumstancial evidence that indicates that R1b as well as R1a were involved in some of the original PIE cultures. I'd actually be quite surprised if at least a little I or J wasn't too. Those lineages may not have survived until today, though. I don't know.

Ialem, you are not doing this, but I do resent when some people cry some kind of foul of a political nature just because of a different point of view than their own.
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« Reply #16 on: May 30, 2012, 11:11:29 AM »

... "Paleolithic R1b" ..... Let's see if I can summarize it.

R1b-M269 arises in Asia in the distant Paleolithic past. Some of its carriers leave all their closest genetic cousins in the old homeland and trek across Europe or perhaps North Africa to arrive in Iberia in time to hole up there for the LGM. At some point this now-western R-M269 becomes mostly R-M412/L51. When it emerges from its LGM hibernation, it spreads eastward and northward into the rest of Europe in that form.

When the Neolithic Revolution occurs, R-M412 initially heads for the hills and tries to avoid the bearers of the strange new technology. Later, carriers of R-M412 learn how to farm and raise livestock and somehow out-reproduce the original Neolithic farmers. They eventually defy all the odds and become the dominant y haplogroup in most of Europe.

At one or more points during the lengthy European saga of R-M412, most of its bearers die off, leaving only a handful of males or perhaps just one male to transmit it to later generations. These "genetic bottlenecks" create the "illusion" of reduced age for western R-M412, but, rest assured, it really is of the greatest antiquity there.

Meanwhile, back in old Asia, the R-M269 xL51 stuff is still around, separated from its distant western cousins now by about 12k years.

I think you summarized the problems I have with "R1b is Paleolithic in Europe" hypotheses. They are clearly not parsimonious in terms of what had to have happened for them to be true.  Rb1 must have been extremely lucky to survive the advanced incomers, but only to within a whisper of their extinction to roar back fully equipped with the new cultural practices and some advantage.

I think a couple of other factors could also be added. One, R1b has been unlucky enough to remained hidden in Europe aDNA findings during the early to pre-Neolithic ages. Two, other European haplogroups show greater diversity so diversity does not "dead end" or completely "saturate" 4-5K ybp....

Well, nothing is impossible so certainly R1b could have been Paleolithic in Europe... although that doesn't mean the R1b-L51 (M412) of today came from Western Europe R1b (M343) lineages.  

Thanks, Jean L, for posting the links and bringing this to attention. I will read through it.
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« Reply #17 on: May 30, 2012, 11:23:46 AM »

... My overall impression is very positive, at least it supports most of my points of view....
Maybe it is just me, but I think the assessment of the paper should be on the evidence, the analysis and the logic.  Whether it agrees with one point of view hopefully is not a big deal. We just want to get the best hypothesis of what happened and if this paper helps us understand that, it is good.  I'm glad for the additional focus on R1b.
  I agree with your comment re: the merits of the paper.  That said, there has been a lot of crow on the DNA forums when the myres/balaresque papers were published and then foul when Busby came out. Not that I'm in the same league as Machiavelli, I do think that he and I among others have been contrarians to the views held by yourself and rms2.

Until DNA came around, the archaeological views of western europe re Aurignacian, Gravettian eras and subsequent descendants held sway and age was guestimated.  Recent carbon dating has given us a much better arechaeological timeframe to fit the DNA data into.  But now we have all these haplogroup flavors to deal with and who came first and when is the dominant question.  I for one am not even sure the ISOGG framework for hgs will stand the test of time?  As several have mentioned this is more of a review paper than an advancement in our level of understanding.  But, it does vote for certain points of view over others and completely omits any discussion of Variance.  Why?

I think this paper is a product of academia as it is today, warts and all.  I believe good science will prevail in the end.  JMHO.
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« Reply #18 on: May 30, 2012, 11:25:10 AM »

I believe good science will prevail in the end.  JMHO.

I absolutely agree. It may take time and this is all just part of the process.


Are you saying they ignore DNA diversity?
...  As several have mentioned this is more of a review paper than an advancement in our level of understanding.  But, it does vote for certain points of view over others and completely omits any discussion of Variance.  Why?

Why do we have to ask why?  If they ignore diversity, don't they explain why they ignore and why whatever techniques they are using are better? It's not like DNA diversity is never analyzed in these papers. Hopefully, I misunderstand your statement.
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« Reply #19 on: May 30, 2012, 11:41:46 AM »

Appears to be a nice summary of all the data up until April, 2012 concerning haplogroups in Europe and the Caucasus, touches everything from Balaresque.et.al.2010 to Myres.et.al.2010, to Busby.et.al.2012.

Different genetic perspectives on human history in Europe and the Caucasus: the stories told by uniparental and autosomal markers

Quote from: Mari Järve

Conclusions

  • The mutation M458, representing a founder effect around the Mesolithic/Neolithic transition in Central and East Europe, separates most of the European R1a carriers from the spread of this Y chromosome haplogroup that spans from South Asia to Siberia and Europe.
  • In West Europe another major Holecene era founder effect is denoted by the mutation M412 within the Y chromosome haplogroup R1b, and the spatial and temporal pattern of a sub-clade within R1b-M412 is in close correlation with the spread of the Linear Pottery Neolithic culture.
  • Populations of the Caucasus are autosomally much more uniform than might be expected from their diverse linguistic and ethnic backgrounds. Conversely, the variation of Caucasian Y chromosome lineages exhibits sharp differences between populations and sub regions, likely due to founder effects and genetic drift in (patrilineally) isolated populations.
  • The Caucasus has not served as a corridor for the movement of people from Near/Middle East to East Europe or to Europe in general. Instead, there is a genetic continuity from the Near Eastern to East European populations along the western coast of the Black Sea, suggesting a predominant trajectory of the flow of genes and humans.
  • Y chromosome STRS with longer repeat units have a lower rate of evolution, in some cases making them better suited for population genetic studies than their counterparts with shorter repeat units.

Also from the same author, and apparently the source of most of Myres.et.al.2010 data:

Refining the phylogeny and phylogeography of the human Y chromosome haplogroup R1b1b
The papers are from a researcher of Tartu University-Estonia
Interesting like synthesis of studies, but according to the knowledge of SNPs in 2008. Now, in Europe, in more of the R1a1a1g1-M458 branch (Central Europe, peak in Central,South Poland), Bohemia), 3 important branches have been found : R1a1a1i-L664 (Germanic), R1a1a1g1-Z280 (Eastern and central Europe), R1a1a1g3 (Western and North Europe). Asiatic R1a is dominated  by the big branch R1a1a1h-Z93.  

Conclusions of the other paper :
"R1b1b" = R1b1a-P297
"R1b1b1" = R1b1a1-P73
"R1b1b2" = R1b1a2-M269
M412 = R1a1a2a1-L11
M466 = R1a1a2a1a1b3-U152
Quote from: Mari Järve

1. The two main sub-hgs of the Y chromosome hg R1b1b, R1b1b1 and R1b1b2, differ
in age and geographic distribution:
• R1b1b1 is a rare and older lineage (coalescence age 27,233±13,060 years),
found at low to moderate frequencies among Eastern European, Turkic and
Caucasian samples, being totally absent in Western Europe;
• R1b1b2 is considerably younger (coalescence age 18,301±3,566 years) and
common in Western Europe, but also spread in some of the Bashkir populations;
2. The two-partite spread of sub-hg R1b1b2  is mostly explained by the novel SNP
marker M412, which has its ancestral state in the majority of the eastern R1b1b2
samples (the R-M269* lineage), and its derived state in the absolute majority of the
western R1b1b2 samples (the R-M412 lineage and its sub-lineages);
3. The sole notable exception to the western spread of the R-M412 lineage, the
northern Bashkirs, who exhibit an uncommonly high frequency of sub-hg R-M466
(inside the R-M412 lineage), appears to be the result of a strong founder effect, as
these samples also have nearly identical STR haplotypes;
4. The M412 mutation has a likely Western European origin, possibly being a marker
of the recolonisation from an isolated population nucleus in the Iberian peninsula
after the LGM 13-20 kya (Semino et al. 2000);
5. Recalibrating the effective mutation rate of STR markers of 6.9·10-4  per 25 years
(Zhivotovsky et al. 2004) based on the variances of 15 markers of the Applied
Biosystems AmpFlSTR® Yfiler™ Kit had very little effect, but the calculations
suggested that the mutation rate of penta- and hexanucleotide STR markers is
significantly lower, estimated as 2.4·10-4 per 25 years;
6. As illustrated by an analysis of  of the STR haplotypes of sister clades R1b1b and R1a, STR markers, including penta- and hexanucleotide microsatellites, can be used to distinguish Y chromosome hgs and, in some cases, subdivisions within hgs, without the help of SNP marker data.
For 5 and 6, I suppose these results are also found in different tables of mutation rate for each STR. This can be linKed  to a lot of workS and discussions about the validity to calculate dates by the divergence of STRs
For 4, the author Mari Järve refers to the paleolithic western origin of R1b-M412/L11 and its sub-branches. Very controversial by fans of neolitic/chalcolitic oriental origins. Personally, although no present scientifiv proof supports it, I guess R1b came to western europe with Gravettians from South Siberia (35,000BP), our Esthonian author thinks Gravettian was the culture of Hg I coming from Near East. I guess hg I came from Middle East/Zagros (45,000bp)with the Proto-Aurignacian derived from Zagros Baradostian.  

For 1,2,3, Bashkirs are a very interesting population. Maybe, indicating the origin of R1b : peak of R1b1a1-M73 in South-East Oural ; presence of "old" branches  R1b=M269, R1b-L23, R1b-L11 isolated in this region of Eurasia. But presence of new  branchd R1b-U152 in  North Oural  with haplotype divergence showing  a recent founding effect is troubling.  Bashkir U152/M466 exists in a small Bashkir trinbe in Perm Krai in Central-West Oural.

There is some Z280+ and Z283+ in Central Asia. Whether that is ancient or recent admixture is another sotry.

I also don't get why you think the  Proto-Aurignacian and ydna I come from the Zagros. There is close to zero I in that area. And no one has ever found IJ.

I'm curious on your thoughts on M73 and what brought it to Central Asia. my theory is that proto Turks picked it up on their way to Central Asia but others have suggested it migrated east with Proto Indo-Iranians.
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« Reply #20 on: May 30, 2012, 11:52:55 AM »

I think you summarized the problems I have with "R1b is Paleolithic in Europe" hypotheses. They are clearly not parsimonious in terms of what had to have happened for them to be true.  Rb1 must have been extremely lucky to survive the advanced incomers, but only to within a whisper of their extinction to roar back fully equipped with the new cultural practices and some advantage.

Well, doesn’t the steppe hypothesis propose that R1b-L23(xL51) suddenly became the new deal, and swiped all the G2a farmers that had been in Europe for millennia. What is the difference between that line of thinking, and assuming that after a while HG in Western Europe managed to bounce back. Are HG in the Steppe special compared to those in Western Europe?

I think a couple of other factors could also be added. One, R1b has been unlucky enough to remained hidden in Europe aDNA findings during the early to pre-Neolithic ages. Two, other European haplogroups show greater diversity so diversity does not "dead end" or completely "saturate" 4-5K ybp....

What is the age of I1 in Europe? Not the interclade age of I1 and I2, but the intraclade age of I1, it is 5000 ybp per the table you posted from Marko H. What is the intraclade age of R1b-L150 5700 ybp per the same datasheet. So what happened to I1, which Afaik is supposed to be one of the few Mesolithic haplogroup, why is I2 much older than I1, could it be because good old I2 knew better, and happened to tag alone with the incoming farmers, whereas I1 suffered the same fate as the R1b-L23 bearers in Western Europe?

Again, I feel like I am repeating myself here, if R1b-L23 doesn’t show up in Cardial Catalonia, or Pre-Beaker Southern France, could it be because it was still in the Western fringes of the Atlantic, think Pyrenees, Basque Country, Brittany. 

I might be wrong, but I say that R1b-L23 pre-Bronze age is more likely to be found both in the Atlantic fringes, and in the Eurasian Steppe. Yes!! I am talking about two dispersals of R1b, one R1b-L150+ from Western Europe, and one of R1b-L23(xL150) from the Steppes, the latter was likely Indo-European speaking, the former wasn't.
 
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« Reply #21 on: May 30, 2012, 11:56:45 AM »

I believe good science will prevail in the end.  JMHO.

I absolutely agree. It may take time and this is all just part of the process.


Are you saying they ignore DNA diversity?
...  As several have mentioned this is more of a review paper than an advancement in our level of understanding.  But, it does vote for certain points of view over others and completely omits any discussion of Variance.  Why?

Why do we have to ask why?  If they ignore diversity, don't they explain why they ignore and why whatever techniques they are using are better? It's not like DNA diversity is never analyzed in these papers. Hopefully, I misunderstand your statement.
  As I said above this is a long paper which I haven't read in detail, so I will not comment in detail; just at the general observation level.

re: diversity, I don't have the same confidence in diversity that you do.  It only estimates coalescence age not TMRCA.  It weights its estimates by the properties of the entries, which may not represent the original distribution at all.  I'm afraid that all the current diversity estimates are biased by the population samples available.  We know the population has grown tremendously in the last few K years.  If you argue the entries are all descendants of a few "successful" ancestors (the genghis khan bias), then you are biasing toward those haplotypes; If you argue the coalescent entry hypothesis then again you are using a few successful entries who started a broad population expansion.

I believe there are outliers, who get washed out in the statistical bath of diversity who probably more represent the age of subclades than diversity does.  JMHO.
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« Reply #22 on: May 30, 2012, 02:43:45 PM »

The map of U106 (aka M405) is completely wrong. A peak in NW Switzerland with decreasing frequency towards the lower Rhine goes against all known studies, including Myres.

And the map for U152 (aka M466) is also completely wrong - highest frequency in SE France and more frequent in most of France than Italy? I think they screwed up the x and y values while applying the Kriging technique on their maps.
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« Reply #23 on: May 30, 2012, 02:47:35 PM »

I believe good science will prevail in the end.  JMHO.

I absolutely agree. It may take time and this is all just part of the process.


Are you saying they ignore DNA diversity?
...  As several have mentioned this is more of a review paper than an advancement in our level of understanding.  But, it does vote for certain points of view over others and completely omits any discussion of Variance.  Why?

Why do we have to ask why?  If they ignore diversity, don't they explain why they ignore and why whatever techniques they are using are better? It's not like DNA diversity is never analyzed in these papers. Hopefully, I misunderstand your statement.
 As I said above this is a long paper which I haven't read in detail, so I will not comment in detail; just at the general observation level....

Okay, I thought your question "why?" was important and pointing to something meaningful about the paper.  I guess not.
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« Reply #24 on: May 30, 2012, 02:58:52 PM »

I think you summarized the problems I have with "R1b is Paleolithic in Europe" hypotheses. They are clearly not parsimonious in terms of what had to have happened for them to be true.  Rb1 must have been extremely lucky to survive the advanced incomers, but only to within a whisper of their extinction to roar back fully equipped with the new cultural practices and some advantage.

Well, doesn’t the steppe hypothesis propose that R1b-L23(xL51) suddenly became the new deal, and swiped all the G2a farmers that had been in Europe for millennia. What is the difference between that line of thinking, and assuming that after a while HG in Western Europe managed to bounce back. Are HG in the Steppe special compared to those in Western Europe?

This reminds of political discussion where instead of defending one's view, a politician (apparently because there is no good defense) just moves onto attack mode on other alternatives, preferrably strawman alternatives that are easy to attack.

I don't know if R1b-L23xL51 came from the Steppes.  I think legitimate cases can be made in the context of cultural movements that R1b-L23 lineages expanded westward from either the Steppes, SE Europe, Anatolia or even the Near East.   I don't know what is most likely.

I think a couple of other factors could also be added. One, R1b has been unlucky enough to remained hidden in Europe aDNA findings during the early to pre-Neolithic ages. Two, other European haplogroups show greater diversity so diversity does not "dead end" or completely "saturate" 4-5K ybp....
.....
Again, I feel like I am repeating myself here, if R1b-L23 doesn’t show up in Cardial Catalonia, or Pre-Beaker Southern France, could it be because it was still in the Western fringes of the Atlantic, think Pyrenees, Basque Country, Brittany.  

I might be wrong, but I say that R1b-L23 pre-Bronze age is more likely to be found both in the Atlantic fringes, and in the Eurasian Steppe. Yes!! I am talking about two dispersals of R1b, one R1b-L150+ from Western Europe, and one of R1b-L23(xL150) from the Steppes, the latter was likely Indo-European speaking, the former wasn't.

Do you have reason why you think R1b-L150+ was lurking along the Atlantic fringe before and during the LBK and Cardial Neolithic advances?

We know for certain that L150+ and L23+ L150- lineages had one Most Recent Common Ancestor who was L23+ L150-. Where and when do you think the MRCA for R1b-L23 (both L150+ and L150-) was?

Your split (east/west) personality for L23 scenario is about to get quite difficult.  I think you will have to place the L23+ L150- MRCA in Central Europe for him to send children both to the Atlantic and Caucasus in very quick fashion at a time when transportation was worse than it was post Neolithic.
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