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MitchellSince1893
02-11-2015, 08:20 PM
Excerpts from the new paper on P312.


I0806 (Bell_Beaker_LN)
The individual was assigned to haplogroup R1b1a2a1a2 based on mutation P312:22157311C→A.
Two Bell Beaker individuals from Kromsdorf, Germany were previously determined2 to belong to
haplogroup R1b.
The individual also has upstream mutations for R1 (P236:17782178C→G), R1b1
(L278:18914441C→T), R1b1a2 (F1794:14522828G→A), and R1b1a2a1 (L51:8502236G→A). Its
haplotype is ancestral for R1b1a2a1a2a1a1a (S1217:7193830C→G, Z262:16320197C→T),
R1b1a2a1a2c1a (DF49:22735599G→A), R1b1a2a1a2c1a1 (DF23:17774409G→A), R1b1a2a1a2c1f1
(L554:15022777A→G), R1b1a2a1a2c1f2 (S868:19033817T→C), R1b1a2a1a2c1i
(CTS6581:16992602T→C) and R1b1a2a1a2c1l1a1 (CTS2457.2:14313081C→T).


I0806 Bell_Beaker_LN Bell Beaker LN Quedlinburg VII 2, Germany; QLB28b, feature 19617 2296-2206 cal BCE (MAMS 22820) Germany M H1 R1b1a2a1a2

Is this the earliest confirmed P312 sample at ~4250 ybp?
My estimate, based on SNP counting method, is P312 is about 4740 years old (+/-750 years)


I0099 Halberstadt_LBA Late Bronze Age LBA Halberstadt-Sonntagsfeld, Germany; HAL36C, grave 40, feature 1114 1113-1021 cal BCE (MAMS 21484) Germany M H23 R1a1a1b1a2 337566

How doos this age and location further our understanding of P312?

VinceT
02-12-2015, 07:28 AM
I0099 is R1a. :)

I hope they can do further testing on I0806. It would really be nice to know if he's under any of the known R-P312 sub-clades.

BTW, there are about 18 SNPs between R-P312 and R-L23.

5 at R-L51:
- PF6535
- PF6414
- L51/M412/PF6536/S167
- CTS8595/YSC0001291
- CTS10373/FGC39/PF6537

13 [or 14] at R-L11:
- FGC796/Y101/Z8159
- PF6415
- PF5856
- PF6540/YSC0000082
- S26903 [unconfirmed]
- L52/PF6541
- L151/PF6542
- PF6543/S1159/YSC0000191
- CTS7650/FGC44/PF6544
- PF6538
- L11/PF6539/S127
- P311/PF6545/S128
- P310/PF6546/S129
- CTS10353/S1175/YSC0001249

MitchellSince1893
02-12-2015, 12:54 PM
I0099 is R1a. :)
...

Oops you are right. I will edit my original post.


BTW, there are about 18 SNPs between R-P312 and R-L23 I had 13 so the additional 5 would add about 400 years to age of L23

rms2
02-12-2015, 12:57 PM
I wonder if L51, or the L23 ancestral to it, did not leave the PC steppe in one of Gimbutas' first two Kurgan waves to move west. Samara, after all, is pretty far east, and Yamnaya, if I recall correctly, was the third and final wave.

Anyway, here are a couple of images I posted on another thread that are relevant to a possible Yamnaya-Beaker connection via Vucedol (Gimbutas derived Beaker from Vucedol).

3771 3772

Those images come from the paper, Transition to the Bronze Age: Issues of Continuity and Discontinuity in the First Half of the Third Millennium BC in the Carpathian Basin (https://www.academia.edu/5717048/Transition_to_the_Bronze_Age_Issues_of_Continuity_ and_Discontinuity_in_the_First_Half_of_the_Third_M illennium_BC_in_the_Carpathian_Basin).

alan
02-12-2015, 01:50 PM
It always seemed likely that Kromsdorf c. 2550BC M269xU106 was either L11 or P312 to me although we cannot prove it.

alan
02-12-2015, 02:34 PM
I wonder if L51, or the L23 ancestral to it, did not leave the PC steppe in one of Gimbutas' first two Kurgan waves to move west. Samara, after all, is pretty far east, and Yamnaya, if I recall correctly, was the third and final wave.

Anyway, here are a couple of images I posted on another thread that are relevant to a possible Yamnaya-Beaker connection via Vucedol (Gimbutas derived Beaker from Vucedol).

3771 3772

Those images come from the paper, Transition to the Bronze Age: Issues of Continuity and Discontinuity in the First Half of the Third Millennium BC in the Carpathian Basin (https://www.academia.edu/5717048/Transition_to_the_Bronze_Age_Issues_of_Continuity_ and_Discontinuity_in_the_First_Half_of_the_Third_M illennium_BC_in_the_Carpathian_Basin).

I think if we chase the peoples/languages and accept there is huge discontinuity in geography then it reveals that both Centum languages in the west and apparently satemised Balkans branch groups like Armenian and Albanian/Dacian have/had a lot of L23xL51 and little L51 and derived. I suppose it is possible that those languages/tribes hung around the steppe longer than L51 and the reason could be that they were located around Samara and that part of the steppe rather than further west in the steppes.

We have got into the habit of thinking that L23xL51 clades are older than L51 but that may be a wrongheaded. In reality it is the earlier branching of IE - lets say the case of Tarim and Tocharian is too hypotetical to be useful- Celtic, Italic and Germanic which are clearly associated with L11 derivatives not L23xL51. The languages which tend to be associated with the latter are Balkans and Armenian languages. Indeed one centum language, Greek is also.

So, it kind of suggests a sequence of waves to me with Celtic-Italic-Germanic breaking off first and linked to L51 and the space they left being filled with L23xL51 types, some of whom broke off before Satemisation - Greek-and others of which remained on or hard against the steppes long enough to be satemised before spreading west and south -i.e. Armenian, Albanian and perhaps Thracian and Dacian. I have noticed its common to see the Greeks and perhaps Thracians as relatively late splits from the steppes.

So perhaps the more easterly L23xL51 types didnt move into the Ukraine vacuum and then the Balkans until L51/L52 had left the steppes. Contrary to commonly help opinion, with the exception of Armenians, L23xL51 is a great deal more common in the north Caucasus than the south so perhaps some of it ended up there. As for M269xL23 its common in the Balkans among Albanians and also Armenians of Ararat if we are primarily looking at IE dialects which are both satemised languages with links to the Balkan group of physically to the Balkans. So it seems to also have a similar history to L23xL51 and perhaps it also was more easterly within the steppes and therefore late arriving in the Balkans etc. This may seem counterintuitive to phylogeny but it makes perfect sense.

I think this new data and what it means for the SNP counting ages of various R1b clades from L23 to P312 is going to help us rule in and out some of the archaeological options we have been chewing over.

alan
02-12-2015, 02:44 PM
Looking around the net at other sites on this paper is an incredible lesson on how pride can be very ugly and how people will argue black is white if something doesnt suit their identity. Also how seriously lacking in class some people are.

alan
02-12-2015, 03:54 PM
I wonder if L51, or the L23 ancestral to it, did not leave the PC steppe in one of Gimbutas' first two Kurgan waves to move west. Samara, after all, is pretty far east, and Yamnaya, if I recall correctly, was the third and final wave.

Anyway, here are a couple of images I posted on another thread that are relevant to a possible Yamnaya-Beaker connection via Vucedol (Gimbutas derived Beaker from Vucedol).

3771 3772

Those images come from the paper, Transition to the Bronze Age: Issues of Continuity and Discontinuity in the First Half of the Third Millennium BC in the Carpathian Basin (https://www.academia.edu/5717048/Transition_to_the_Bronze_Age_Issues_of_Continuity_ and_Discontinuity_in_the_First_Half_of_the_Third_M illennium_BC_in_the_Carpathian_Basin).

I have suspected that some R1b could been involved in wave I or the Suvorovo wave of Anthony. As far as I recall though, this was a very small wave with small numbers of graves having been found. So its hard to know what y lines were involved and of course the model of Anatolian passing from the steppes to the Balkans to Anatolia in this period has always been a bit light on archaeological evidence for the taste of many. Then again in archaeological terms there is no actual Yamnaya sweep across Europe but somehow the Yamnaya genes moved, presumably through intermediary cultures.

razyn
02-12-2015, 04:11 PM
I had 13 so the additional 5 would add about 400 years to age of L23

I think this is the crazy part of estimating TMRCA by counting SNPs. If the SNPs don't make distinct nodes and leave separate branches, what evidence do we have that they have occurred serially? As distinguished from 13 happening to one guy, at one time and place; and all of his patrilineal descendants having that cluster of 13 mutations (at different loci) -- whether born in the very next generation, or a thousand years later? If the latter were the case for these 5 (e.g.), they would of necessity add just one generation (or birth event), not five times the observed average rate of 80 years between mutations. Which (average rate) btw gets shorter every time we have a better testing method, find another multitude of SNPs, and distribute them along the trees we have been building.

Megalophias
02-12-2015, 06:12 PM
I think this is the crazy part of estimating TMRCA by counting SNPs. If the SNPs don't make distinct nodes and leave separate branches, what evidence do we have that they have occurred serially? As distinguished from 13 happening to one guy, at one time and place; and all of his patrilineal descendants having that cluster of 13 mutations (at different loci) -- whether born in the very next generation, or a thousand years later? If the latter were the case for these 5 (e.g.), they would of necessity add just one generation (or birth event), not five times the observed average rate of 80 years between mutations. Which (average rate) btw gets shorter every time we have a better testing method, find another multitude of SNPs, and distribute them along the trees we have been building.

Mutations do not accumulate at a steady rate; they happen randomly. So yes, a whole bunch can happen at once, or they can be spread over a long time. If you look at a Y haplogroup tree that shows the branch lengths, you can see that the number of mutations in a lineage from a given node to the present - a fixed amount of time - can vary wildly. You can have no SNPs at all on one line and 12 on another. If you estimated the age of the node from only one branch in these sort of cases, you'd get wildly different (and erroneous) dates.

Using an average rate just gives the most likely time, not a certain date. Most of the time the number of mutations will be close to the expected value and not an outlier, so usually your estimated date will not be too far off. If you have many branches descending from one node independently, then you can average them out and hopefully get closer to the true number that way. But it's still just a best estimate with large error bars.

MJost
02-12-2015, 07:32 PM
I think this is the crazy part of estimating TMRCA by counting SNPs. If the SNPs don't make distinct nodes and leave separate branches, what evidence do we have that they have occurred serially? As distinguished from 13 happening to one guy, at one time and place; and all of his patrilineal descendants having that cluster of 13 mutations (at different loci) -- whether born in the very next generation, or a thousand years later? If the latter were the case for these 5 (e.g.), they would of necessity add just one generation (or birth event), not five times the observed average rate of 80 years between mutations. Which (average rate) btw gets shorter every time we have a better testing method, find another multitude of SNPs, and distribute them along the trees we have been building.

You are correct questioning how the SNP counting is done. But consider if all blocks of SNPs (different loci) are truly non-serial, the entire age of man would be much unrealistically younger. Some SNPs have occurred within the same generation but, just like STRs, it would not be the norm. If a number of SNPs shows an average of 130-175 years calculated from calibrated carbon dated sources, converted to 'x' generations or birth events this is the average when a mutation could occur.

Researchers have used Sanger/PCR tested SNPs to confirm original discovered SNPs in the entire tree. Only recently, we are including ChrY NGS results that, upon review and comparison to other results, have discovered new SNPs that are increasing the number of SNPs under various known SNPs. Its when we are noticing new branch splits, those new nodes help change known TMRCAs of existing nodes. R branch has shown some key changes in the various Blocks (those list of SNPs that can not be ordered) of SNPs but is the same age no matter how that age is determined.

With NGS, we are seeing new SNPs that may or may not be stable SNPs until we have 1000's of results to compare but 100's are a great start and, which I would trust as important stable ancient mutations. But considering all the new discoveries, I would assume that we are hitting or should be see a serious diminished return in finding new ancient SNPs under each major ChrY branches such as R.

Technically, I would now take all the ancient Sanger and NGC SNPs under R and then take a know massive branch such as P312 and come up with a 'Rho' of Sanger and any separately confirmed stable NGS below and recalculate the R tree based on Mal'ti boy's Carbon dated age.

I count (out of date and is probably more by now) 108 SNPs under R down to DF13, which are Sanger/PCR and new stable NGS'ed SNPs, plus my 29 Sanger Sequence Full Y genome results and NGS stable SNPs below DF13 (Two or more confirmed positive with 27 SNPs leaving two private Sanger'ed SNPs.) This then totals 137 SNPS and minus five SNPs using Mal'ti boy's age of 24K ybp equates to 175.1 years per SNPs as an average. But using another study's 18,500 suggested brings the average down 135 year per mutation. Again showing what is used to calibrate the R1, the parent of R1b, as 18,500ybp Karafet et al there are 89 SNP down to DF13, add 29 equals 118 SNPs or 157 years per SNP. So as you see, calibrating is everthing.

MJost

rms2
02-12-2015, 07:34 PM
Looking around the net at other sites on this paper is an incredible lesson on how pride can be very ugly and how people will argue black is white if something doesnt suit their identity. Also how seriously lacking in class some people are.

Yep. You've got the folks holding out for the old FC Ice Age Refuge who will seize on the El Trocs R1b1 as "the great Iberian Hope"; the "aR1an" crowd who will make a big deal out of the fact these seven Yamnaya guys all came from the Samara region (must be a fluke!) and most of them were Z2103 (and thus not the ancestors of Western Europeans); and, lastly, a smaller group of R1b guys who are determined to rub the R1a guys' faces in these results.

All three are clearly not right.

MitchellSince1893
02-12-2015, 10:03 PM
Mutations do not accumulate at a steady rate; they happen randomly. So yes, a whole bunch can happen at once, or they can be spread over a long time. If you look at a Y haplogroup tree that shows the branch lengths, you can see that the number of mutations in a lineage from a given node to the present - a fixed amount of time - can vary wildly. You can have no SNPs at all on one line and 12 on another. If you estimated the age of the node from only one branch in these sort of cases, you'd get wildly different (and erroneous) dates.

Using an average rate just gives the most likely time, not a certain date. Most of the time the number of mutations will be close to the expected value and not an outlier, so usually your estimated date will not be too far off. If you have many branches descending from one node independently, then you can average them out and hopefully get closer to the true number that way. But it's still just a best estimate with large error bars.

I caution against those tempted to count their own private SNPs to establish dates as the number of SNPs in individual lines can very greatly. However, as you said taking an average from many lines can negate the outliers.

If additional testing was done on this P312 sample to determine how many additional SNPs are present e.g. he's turns out to be P312>U152>L2 but is negative for all known sub branches of L2, then we could get an approximate date for L2.

Knowing this date, we could look at all the BigY and FGC results and get an average number of SNPs for each below L2 in this example. On some lines there may be 20 SNPs below L2, on others there may be 60+, but the median may be 40 for BigY and 45 for FGC testers.

One could estimate the ages of other SNPs that don't currently have archaeological results. Staying with the L2 example, one could estimate the age of L2's brother branches e.g. Z36 or for that matter estimate the age of U152's brothers L21 or DF27, or one of their branches.

MJost
02-13-2015, 01:52 AM
I0099 is R1a. :)

I hope they can do further testing on I0806. It would really be nice to know if he's under any of the known R-P312 sub-clades.

BTW, there are about 18 SNPs between R-P312 and R-L23.



Here is the SNP counts of the R tree. MJost



SNPs in Block
Chr Y HG


23
R


4
R.1-Y482


44
R1


1
R1b-M343/PF6242


2
R1b1.1 M415/PF6251 * L278


1
R1b1.2 L389/PF6531


2
R1b1a P297/PF6398 * L320/PF6092


7
R1b1a2 - M269


3
R1b1a2a - L23


4
R1b1a2a1 - L51


8
R1b1a2a1a - L11


2
R1b1a2a1a2 - P312


6
R1b1a2a1a2c - L21


2
DF13


29
FGC5494

VinceT
02-13-2015, 04:07 AM
^ Some of them, yes. I have a list of at least 147 from R-P297 through R-L23, and an additional 15 at or below R-L389 and above R-L23. Then 56 more at R1b-M343 or R1b1-M415, and another 67 at R1-M173, and 66 at R-M207. These were mostly pulled from Greg Magoon's 1KGP study.

rms2
02-13-2015, 01:04 PM
I think it likely that the Quedlinburg Bell Beaker P312 man was P312*, but I don't know that for sure, obviously. It's interesting that not only is Beaker now three-for-three R1b, but it is also three-for-three U106- (in areas where U106 is quite frequent today), which is consistent with its alleged connection to Italo-Celtic.

Piquerobi
02-13-2015, 01:08 PM
^ They should also test the Kurgan remains near Hungary. The Danube route is often mentioned as a penetration path, with many Kurgan burials. And they have been associated with the spread of Italo-Celtic languages. Gimbutas' location of the origins of the Bell Beakers' movements westwards is somewhere near that region.


The Bell Beaker complex, an offshoot of the Vucedol bloc (more precisely of the Zok-Mako group in Hungary) continued Kurgan charateristics. The Bell Beaker of the second half of the 3rd millenium BC were vagabondic horse riders and archers in much the same way as their uncles and cousins, the Corded people of northern Europe and Catacomb-grave people of the North Pontic region. Their spread over central and western Europe to the British Isles and Spain as well as the Mediterranean islands terminates the period of expansion and destruction.
Gimbutas

rms2
02-13-2015, 01:13 PM
Right. I would really like to see that. These kinds of monumental studies leave one thirsting for more. I hope we don't have to wait years for another round of ancient y-dna results!

Piquerobi
02-13-2015, 01:16 PM
David Anthony speaks of a high number of Kurgan burials in Hungary sharing strong archeological and anthropological similarities back to the steppes. They got there via the Danube and their track up to Hungary has already been established by archeologists. Testing them would be key. Not only the Corded Ware remains. I believe they may be associated with Italo-Celtic IE languages as well as with Bell Beakers and R1b-M269-L23-L51-P312+.

rms2
02-13-2015, 01:22 PM
David Anthony speaks of high number of Kurgan burials in Hungary sharing strong archeological and anthropological similarities back to the steppes. They got there via the Danube and their track up to Hungary has already been established by archeologists. Testing them would be key. Not only the Corded Ware remains.

I agree. After your initial post (a couple of posts back) it occurred to me that the Yamnaya pathway west is the place to look for L51 and L11, not way out east in Samara, although they could turn up near there, as well. The Carpathian Basin, the Hungarian Plain, and the Danube Valley, those are the hotspots.

Obviously, the ancestors of today's Western European R1b's went west at some point.

rms2
02-13-2015, 07:54 PM
I missed the statement in quotes below and thought Haak et al merely failed to test the Quedlinburg Beaker P312+ for U152, DF27, and L21. I was wrong about that. It was pointed out to me that they tested all the ancient male remains for the full panoply of y-dna SNPs listed on ISOGG's tree as of April 2013; they just were not able to get reads on many of them.

That makes sense and explains things very well.



The 390k capture reagent targeted all SNPs present in the Y-DNA SNP index of the International
Society of Genetic Genealogy (ISOGG) version 8.22 as of April 22, 2013
(http://isogg.org/tree/ISOGG_YDNA_SNP_Index.html).

So, evidently they just did not get reads for U152, DF27, and L21. Too bad.

rms2
02-14-2015, 07:57 PM
I wanted to point out that Rick Arnold, who posts here only rarely, under the screen name Rick, predicted years ago that Bell Beaker would be mostly P312+. He also said he thought Beaker would prove to be the vehicle for the entry of L21 into the British Isles.

Well, the first two Beaker y-dna results, from Kromsdorf, Germany, turned out to be R1b and U106-, and now a third Bell Beaker man, this one from a site near Quedlinburg, Germany, has tested P312+. They got no-reads for U152, DF27, and L21, unfortunately, so we don't know about his status with them.

Anyway, I hope Rick doesn't mind me taking his name in vain. I think he should get credit for being very smart and obviously prescient, since he called this I think back in early 2008 on the old dna-forums site.

I actually had the honor of meeting Rick in person once several years ago. Super nice guy.

Krefter
02-14-2015, 08:21 PM
Yep. You've got the folks holding out for the old FC Ice Age Refuge who will seize on the El Trocs R1b1 as "the great Iberian Hope"; the "aR1an" crowd who will make a big deal out of the fact these seven Yamnaya guys all came from the Samara region (must be a fluke!) and most of them were Z2103 (and thus not the ancestors of Western Europeans); and, lastly, a smaller group of R1b guys who are determined to rub the R1a guys' faces in these results.

All three are clearly not right.

Surprisingly Maju isn't giving much attention to the Iberian R1b1* sample. He says both the Samara and Spanish R1b1*s probably have nothing to do with modern R1b-L11.

rms2
02-14-2015, 08:27 PM
Surprisingly Maju isn't giving much attention to the Iberian R1b1* sample. He says both the Samara and Spanish R1b1*s probably have nothing to do with modern R1b-L11.

Maybe he has sense enough to realize it's nearly impossible for the Els Trocs R1b1 (M415) to be the ancestor of today's R1b-L11 Western Europeans.

Obviously, this set of mostly Z2103/Z2105 Yamnaya guys aren't our ancestors either, but they are more immediate relatives of ours than Els Trocs, and it is likely that Yamnaya spawned Grandfather L51 or that one of the preceding Kurgan waves west did.

rms2
02-14-2015, 08:55 PM
Here is a pretty good video on the Beaker Folk.


http://videopediaworld.com/video/44732/Indo-Europeans-in-Northern-Europe-12

Rick
02-14-2015, 09:28 PM
I wanted to point out that Rick Arnold, who posts here only rarely, under the screen name Rick, predicted years ago that Bell Beaker would be mostly P312+. He also said he thought Beaker would prove to be the vehicle for the entry of L21 into the British Isles.

Well, the first two Beaker y-dna results, from Kromsdorf, Germany, turned out to be R1b and U106-, and now a third Bell Beaker man, this one from a site near Quedlinburg, Germany, has tested P312+. They got no-reads for U152, DF27, and L21, unfortunately, so we don't know about his status with them.

Anyway, I hope Rick doesn't mind me taking his name in vain. I think he should get credit for being very smart and obviously prescient, since he called this I think back in early 2008 on the old dna-forums site.

I actually had the honor of meeting Rick in person once several years ago. Super nice guy.

Rich, you're very kind to remember, but I'd note that for this one guess I can recall a hundred others I made that were dead wrong. Thankfully the demise of the old forum has obliterated those too from the record.
If you'll all excuse a bit of mutual admiration I'll recall that it was Rich, as stevo back in the day, who first noted the r1a-r1b correlation with the centum-satem divide in IE. That was a real watershed moment in the hobby, as the European Paleolithic continuity theory still held sway at the time. Very few if any gave thought to massive recent migration, and if so certainly it didn't involve R1. Reconsideration of the age of the haplogroups of Europe soon followed. That must have been summer of 2006 or so. It has all been fun to watch since then, with this paper certainly being a milestone.

But we should still keep our conclusions tentative and minds open.