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alan
11-30-2013, 01:27 AM
I have seen some rumours that the Afontova burial is some form of r1a. I only seen it suggested by a poster on Dienekes. If true, the date is not quite the shock some are making out. The Afontova burial is post-LGM c. 15000BC which would not be really mind blowing if it was R1a.

What would be more surprising than the date is the fact that R1a was in Siberia at that date. A lot of folks have tended to think R1a was somehow related to the Upper Palaeolithic groups in European Russia or the Ukraine but I think there has always been indirect evidence that this was not the case.

More interestingly, the technological group that Afantova man is linked to, the microblade late upper palaeolithic of Siberia is thought to have originated somewhere like Altai c. 25000BC and to have expanded north again from there. That actually would give R1a a cultural home in the LGM. As far as I understand the late/post LGM story that Afanatovo man's cultural package was part of was a recolonisation of south central and then even more challenging parts of Siberia, probably from a refuge in somewhere like Altai or further south-east. That would indicate that some of R1, at least R1a remained much further east through the LGM than is normally thought.

This kind of scenario would also potentially allow us to trace the spread of R1a with the spread west of this kind of late upper palaeolithic siberian microblade technology. I will have a dig about. Also there is the interesting diffusion of pottery from very early origins in the far east too to consider although I need to refresh my memory on that.

alan
11-30-2013, 01:49 AM
This discusses the spread of microblade technology into Russia, significantly later than in Siberia and the far east

http://www.phil.uni-greifswald.de/fi...hilin_2010.pdf

ADW_1981
11-30-2013, 02:23 AM
I have seen some rumours that the Afontova burial is some form of r1a. I only seen it suggested by a poster on Dienekes. If true, the date is not quite the shock some are making out. The Afontova burial is post-LGM c. 15000BC which would not be really mind blowing if it was R1a.

What would be more surprising than the date is the fact that R1a was in Siberia at that date. A lot of folks have tended to think R1a was somehow related to the Upper Palaeolithic groups in European Russia or the Ukraine but I think there has always been indirect evidence that this was not the case.

More interestingly, the technological group that Afantova man is linked to, the microblade late upper palaeolithic of Siberia is thought to have originated somewhere like Altai c. 25000BC and to have expanded north again from there. That actually would give R1a a cultural home in the LGM. As far as I understand the late/post LGM story that Afanatovo man's cultural package was part of was a recolonisation of south central and then even more challenging parts of Siberia, probably from a refuge in somewhere like Altai or further south-east. That would indicate that some of R1, at least R1a remained much further east through the LGM than is normally thought.

This kind of scenario would also potentially allow us to trace the spread of R1a with the spread west of this kind of late upper palaeolithic siberian microblade technology. I will have a dig about. Also there is the interesting diffusion of pottery from very early origins in the far east too to consider although I need to refresh my memory on that.

For the most part, those bloggers over at Dienekes' have no inside info whatsoever, and more often than not they are full of nonsense.

parasar
11-30-2013, 02:49 AM
I have seen some rumours that the Afontova burial is some form of r1a. I only seen it suggested by a poster on Dienekes. If true, the date is not quite the shock some are making out. The Afontova burial is post-LGM c. 15000BC which would not be really mind blowing if it was R1a.

What would be more surprising than the date is the fact that R1a was in Siberia at that date. A lot of folks have tended to think R1a was somehow related to the Upper Palaeolithic groups in European Russia or the Ukraine but I think there has always been indirect evidence that this was not the case.

More interestingly, the technological group that Afantova man is linked to, the microblade late upper palaeolithic of Siberia is thought to have originated somewhere like Altai c. 25000BC and to have expanded north again from there. That actually would give R1a a cultural home in the LGM. As far as I understand the late/post LGM story that Afanatovo man's cultural package was part of was a recolonisation of south central and then even more challenging parts of Siberia, probably from a refuge in somewhere like Altai or further south-east. That would indicate that some of R1, at least R1a remained much further east through the LGM than is normally thought.

This kind of scenario would also potentially allow us to trace the spread of R1a with the spread west of this kind of late upper palaeolithic siberian microblade technology. I will have a dig about. Also there is the interesting diffusion of pottery from very early origins in the far east too to consider although I need to refresh my memory on that.

If true, YFull should release soon.
http://www.theapricity.com/forum/showthread.php?102904-Palaeloithic-Siberians-full-DNA-results&p=2133208&viewfull=1#post2133208

alan
11-30-2013, 03:07 AM
Yeah I am suspicious. Its also on the Apricity. Not that I ever look at that site, it just came up when I googled this looking for some more info. It was a couple of days ago and I was wondering how I could have missed something big like that.


For the most part, those bloggers over at Dienekes' have no inside info whatsoever, and more often than not they are full of nonsense.

Generalissimo
11-30-2013, 04:07 AM
It's true, the data from this sample are positive for SNPs from haplogroup Q and R1a-M417. But after M417 they're negative for all downstream markers. So the result looks like an R1a-M417*.

However, if you look at the study, the authors say that this sample is a fairly poor one and also highly contaminated. So it could be another case of a bogus Y-DNA result, like the Neanderthal that came out R1a-Z280 not long ago.

parasar
11-30-2013, 05:24 AM
It's true, the data from this sample are positive for SNPs from haplogroup Q and R1a-M417. But after M417 they're negative for all downstream markers. So the result looks like an R1a-M417*.

However, if you look at the study, the authors say that this sample is a fairly poor one and also highly contaminated. So it could be another case of a bogus Y-DNA result, like the Neanderthal that came out R1a-Z280 not long ago.

Do we have any source on the M417 Gora II as well as the prior Z280?

Generalissimo
11-30-2013, 05:25 AM
A lot of folks have tended to think R1a was somehow related to the Upper Palaeolithic groups in European Russia or the Ukraine but I think there has always been indirect evidence that this was not the case.


More interestingly, the technological group that Afantova man is linked to, the microblade late upper palaeolithic of Siberia is thought to have originated somewhere like Altai c. 25000BC and to have expanded north again from there.

It seems to me as if Afontova Gora represents the eastern end of a continuum that stretched from Europe to pre-East Asian Siberia, just before the entry of East Asians into the Siberian taiga from near the Altai. So if Afonotova Gora was indeed M417*, then Eastern Europeans at the time were also M417*. Not long after that, most of Siberia shifted to N and C.

http://img600.imageshack.us/img600/1925/2a61.png

Unless of course you're also claiming that the bulk of European ancestry, in other words the main West Eurasian ancestral clade, expanded from the Altai post-Ice Age towards the west.

Generalissimo
11-30-2013, 05:27 AM
Do we have any source on the M417 Gora II as well as the prior Z280?

Semargl from Molgen.


I agree with you about the possibility of sample contamination.
He has several positive SNPs Q. The remaining SNPs of haplogroup R1a.
Sample quality is very poor.
I did not want to publish data on this sample, but some people could not resist)
Y.bam weighs 2mb :)

But it's worth noting that the positive SNPs below M417 not.
Unlike Neanderthal man Z280+ :D

alan
11-30-2013, 04:41 PM
I understand M417 is usually dated to about 5000BC so it does look like contamination given the burial is from somewhere around 15000BC. I do hope this doesnt reanimate the zhiv rate zombies by claiming it isnt contamination.


It's true, the data from this sample are positive for SNPs from haplogroup Q and R1a-M417. But after M417 they're negative for all downstream markers. So the result looks like an R1a-M417*.

However, if you look at the study, the authors say that this sample is a fairly poor one and also highly contaminated. So it could be another case of a bogus Y-DNA result, like the Neanderthal that came out R1a-Z280 not long ago.

parasar
11-30-2013, 05:38 PM
I understand M417 is usually dated to about 5000BC so it does look like contamination given the burial is from somewhere around 15000BC. I do hope this doesnt reanimate the zhiv rate zombies by claiming it isnt contamination.

The fact that this M417 is followed by no modern sequences tells me that it is not likely to be modern contamination in the Afontova Gora sequence. Paabo and his team have specifically guarded against such contamination since some earlier episodes. The Q with M417 is problematic though unless there is some error in the current phylogeny.

alan
11-30-2013, 05:54 PM
I am only talking about yDNA at present. It is very easy for a y line to change its autosomal signature. So, I dont really think we can have a clue as to what autosomal DNA was linked to what y lines back in the Palaeolithic except where we get ancient samples.

The archaeology of Siberia and the cultural items with the Mal'ta and Afontova burials show they are two different cultural technocomplexes seperate by the LGM (except around Altai) were involved and the chronology appears to show the abandonment of much of Siberia. I have got to be honest that I expected Afontova to be a different y line, and maybe he was, due to the long hiatus and the apparent east Asia/Altai origins of the culture. At the moment archaeologists have found the microblade technology far earlier in what seems to be the Altai reguge, from 25000BC. So it seems to have developed in Altai during the LGM retreat but only expanded back into Siberia at the end of the LGM. I believe Afontova is one of the early site of this post-LGM culture in that area. So, while I have no fixed views on this and am at the mercy of specialist's opinions on this, it is hard to read anything other than that Afontova related to a group (possibly a Mal'ta related group) who retreated to Altai (and perhaps east Asia) and developed this new technology that re-expanded widely over Siberia around 15000BC. The implication of Afontova being Mal'ta-like combined with the chronological spread and origin of the microblade technology does seem to me to imply that Afontova descended from regugees from the Baikal, Yenessee area who wintered the LGM in the Altai or some other area to the east.

I had guessed to myself that Afontova would be haplogroup Q. There doesnt seem to be any R in Altai other than much later R1a that probably came from the west.

What is interesting is that the microblade technology seen first in Altai seems to spread into Siberia and slowly spread west appearing in the very late Palaeolithic in European Russia. What is even more interesting to me is that some groups features this new technology and others rejected it. There could be some link to bands spreading west from Siberia into Europe and perhaps R1 downstream of that. I also think the late Palaeolithic/Mesolithic spread of pottery across northern Eurasia from east to west is something also worth further consideration.

Rewinding back in time to the Mal'ta boy, he appears to belong to one of the very last generations of the middle upper palaeolithic culture of south-central Siberia, a culture which apparently commenced in the area c. 30000BC. So, he was part of a long standing culture which itself appears to have expanded into Siberia after the early upper palaeolithic groups from c. 40000BC or so had abandoned the area in a previous downturn. The origin of the Mal'ta boy's culture which appeared in Siberia c. 30000BC is very uncertain as far as I can deduce and it is neither easily fitted into either European Aurignacian or Gravettian. More of a parallel thing it appears.


It seems to me as if Afontova Gora represents the eastern end of a continuum that stretched from Europe to pre-East Asian Siberia, just before the entry of East Asians into the Siberian taiga from near the Altai. So if Afonotova Gora was indeed M417*, then Eastern Europeans at the time were also M417*. Not long after that, most of Siberia shifted to N and C.

http://img600.imageshack.us/img600/1925/2a61.png

Unless of course you're also claiming that the bulk of European ancestry, in other words the main West Eurasian ancestral clade, expanded from the Altai post-Ice Age towards the west.

alan
11-30-2013, 06:05 PM
Sorry I am lost. They found indications of both R1a and Q? I have got to be honest that Q is what I thought the Afantova person would be based on a complex of considerations. However, they were clearly concerned about contamination or they would have provided a conclusion on the Afontova Y DNA.


The fact that this M417 is followed by no modern sequences tells me that it is not likely to be modern contamination in the Afontova Gora sequence. Paabo and his team have specifically guarded against such contamination since some earlier episodes. The Q with M417 is problematic though unless there is some error in the current phylogeny.

alan
11-30-2013, 06:09 PM
Has anyone credible discussed the Afontova Y DNA?

parasar
11-30-2013, 06:21 PM
Has anyone credible discussed the Afontova Y DNA?

Semargl (http://www.isogg.org/wiki/YFULL.com http://www.yfull.com ) is eminently credible.


Sorry I am lost. They found indications of both R1a and Q? I have got to be honest that Q is what I thought the Afantova person would be based on a complex of considerations. However, they were clearly concerned about contamination or they would have provided a conclusion on the Afontova Y DNA.

Quote attributed to Semargl "He has several positive SNPs Q. The remaining SNPs of haplogroup R1a."

ADW_1981
11-30-2013, 06:47 PM
Semargl (http://www.isogg.org/wiki/YFULL.com http://www.yfull.com ) is eminently credible.



Quote attributed to Semargl "He has several positive SNPs Q. The remaining SNPs of haplogroup R1a."

Isn't it the negatives we should be worried about? Such as the ones which were found in the R* sample? After all, the 24,000 year old sample had R1b positive SNPs but these were ruled out since some critical ones were missing for R1. If there are similar negatives in the younger sample then maybe it is R* as well.

Jean M
11-30-2013, 07:07 PM
It's true, the data from this sample are positive for SNPs from haplogroup Q and R1a-M417. But after M417 they're negative for all downstream markers. So the result looks like an R1a-M417*.

However, if you look at the study, the authors say that this sample is a fairly poor one and also highly contaminated. So it could be another case of a bogus Y-DNA result, like the Neanderthal that came out R1a-Z280 not long ago.



Semargl from Molgen.


I agree with you about the possibility of sample contamination.
He has several positive SNPs Q. The remaining SNPs of haplogroup R1a.
Sample quality is very poor.
I did not want to publish data on this sample, but some people could not resist)


Since an individual cannot be both Q and R, we can see why the paper's authors reported contamination and did not publish a Y-DNA haplogroup for this sample, and why Semargl did not want to publish the data from this sample and refers to the issue of contamination. The position seems to be that we don't know if the ancient individual was Q and the bones handled by an R1a person or vice-versa or what sort of mix-up or DNA damage has produced this weird result. That is what you are saying David? Makes sense to me.

parasar
11-30-2013, 07:11 PM
Isn't it the negatives we should be worried about? Such as the ones which were found in the R* sample? After all, the 24,000 year old sample had R1b positive SNPs but these were ruled out since some critical ones were missing for R1. If there are similar negatives in the younger sample then maybe it is R* as well.

I went through the Google translated version on the molgen.org forum, and looks like it is indeed R1a1a1. Maximus/Centurion's read can be relied upon. The only issue could be some ancient contamination. I also did not see Q reported.

Excerpts from forum.molgen.org


short (R) P227 + (R) P280 + (R) P285 + (R1) P231-(R1) P234-(R1) P236-(R1) P245-(R1) P294-(R2) M479-
http://forum.molgen.org/index.php/topic,6301.30.html [for Mal'ta MA1]

I'm afraid that all the evidence points to R1a1a. [for Afontova Gora 2]
http://forum.molgen.org/index.php/topic,6301.90.html

not counting the pile SNP level BT CT picture is about the
F
P159
M3716
M3720
M3696
P160
M3678
Y1827
M3636
M3747
M3772

P
M1186
M1232
Y492
L781
Y1796
Y1611
M1256
M1264
M1252
PF5971
M1189

R
Y369

R1
PF6525
Y101

R1a1a
M609
Y1429
CTS11148
PAGE7
M752
M761
M810
http://forum.molgen.org/index.php/topic,6301.105.html

The question remains, what could be R1a1a 17,000 years ago?
http://forum.molgen.org/index.php/topic,6301.105.html

Page7 - R1a1a1
he is one level with SNPs M417 and lies below M198.
There are other dating of the remains: "13,810 + -35 years old by radiocarbon dating"
On the 111-minute tree, the token I get from 10,300 to 12,500 years age M417. Age probably underestimated, since there are only a few relict haplotypes with 111 markers.
http://forum.molgen.org/index.php/topic,6301.105.html

And even as much as 4% "Papuan" - clear evidence of Southeast Asian origin. afontovets And here is really closer to the Volga region.
http://forum.molgen.org/index.php/topic,6301.120.html

alan
11-30-2013, 08:20 PM
Q is kind of what I guessed it might be based on all sorts of archaeological, climate and other genetic considerations. R1a1a must be contamination though just on date alone. It seems a lot less likely on balance of probabilities that Q entered from contamination by Russian archaeologists although its not impossible. It is much rarer than R1a in Russia except in north Siberia and Beringia.

parasar
11-30-2013, 08:47 PM
Q is kind of what I guessed it might be based on all sorts of archaeological, climate and other genetic considerations. R1a1a must be contamination though just on date alone. It seems a lot less likely on balance of probabilities that Q entered from contamination by Russian archaeologists although its not impossible. It is much rarer than R1a in Russia except in north Siberia and Beringia.

That would depend on how many matches there were with Q (if any, as I did not see Maximus report any) and how many with R(1 reported) then R1(2 reported) and then R1a1 (7 reported).
If it were modern contamination we would get many more matches, and a high number would be modern lineages downstream of Page7. We have also got remember that Genetiker found this sample to be much more European shifted than the Mal'ta one.

alan
11-30-2013, 09:29 PM
Then again only part of the y chromosome probably has been picked up so matching would be distorted. It sounds to me like we should follow the authors findings that this is a mixed, confused and partial y chromosome reading and we cannot read anything into it. I am pretty sure that R1a1a doesnt make sense anyway when you take into account the relatively close to root (with only some private SNPs) Mal'ta boy was. It seems to me from what others have said that there would be far too many SNPs between the slightly derived R*Malta boy c. 22000BC and the Afantova guy c. 15000BC for R1a1a to be anything but contamination.


That would depend on how many matches there were with Q (if any, as I did not see Maximus report any) and how many with R(1 reported) then R1(2 reported) and then R1a1 (7 reported).
If it were modern contamination we would get many more matches, and a high number would be modern lineages downstream of Page7. We have also got remember that Genetiker found this sample to be much more European shifted than the Mal'ta one.

alan
11-30-2013, 09:30 PM
I suppose its also worth noting that the earliest branchings of R1a in modern populations do not point to Siberia.

parasar
11-30-2013, 10:10 PM
I suppose its also worth noting that the earliest branchings of R1a in modern populations do not point to Siberia.

That is a good point, and that is what had made me think that western Europe was the likely spot of origin close to the end of LGM.

"Right now, I feel that M417 was born in the vicinity of the North Sea either on the continent or the Isles, but not in Norway, around LGM. With LGM, R1a1 retreated south and east and by 15000ybp was established on the Indus. The R1a1 in the Isles is some relict." http://www.anthrogenica.com/showthread.php?1026-what-is-the-latest-thinking-on-were-R1a-originated&p=10448&viewfull=1#post10448

But the latest Full Genomes reports show that all the main (~99%+) nodes CTS4385, Z283, and Z93 are within a few SNPs (couple of hundred years) of each other. All three types were likely in the same clan, or even camp. So this perhaps mammoth hunting family could have lived almost anywhere from the southern British Isles to North Western America, and moved with the game. Now this makes it possible that one branch of the family just retreated to South Asia directly from Siberia and one moved on to Europe.

parasar
11-30-2013, 11:39 PM
Changing structure from K to R, is clearly pushing the origin of P-R further east.

1. Proposed by Karafet, 2008
http://2.bp.blogspot.com/_ro2ijOk8JWc/R_OzyB6YW8I/AAAAAAAAABo/1lT-OBUGV_o/s1600/ytree.jpg




2. Chiaroni K-M526, 2009 "Diamond indicates position of M526 SNP that now unifies haplogroups KMNOPS."
http://www.pnas.org/content/106/48/20174/F1.medium.gif




3. Magoon Full Genomes, 2013 X and MP

Papuan, HGDP00542) appears to have some interesting implications for the phylogenetic structure around haplogroup M. In particular, the tree shows that the haplogroup M sample shares derived status with haplogroup P samples at several SNP sites, indicating the existence of an “MP” haplogroup upstream of haplogroup P and haplogroup M, and downstream of haplogroup K(xLT)
MP http://1.bp.blogspot.com/-GwlFjqHxuNk/UpPLqLlJnvI/AAAAAAAAJaM/UOjh12yl5Y8/s1600/newtree.png

Generalissimo
12-01-2013, 03:27 AM
So this perhaps mammoth hunting family could have lived almost anywhere from the southern British Isles to North Western America, and moved with the game. Now this makes it possible that one branch of the family just retreated to South Asia directly from Siberia and one moved on to Europe.

I doubt any of the mammoth-steppe hunters belonged to R1a-M417. And I doubt that Z93 arrived in South Asia before the Bronze Age. But Afontova-Gora 2 almost certainly belonged to R and mtDNA U, and so did Sungir. We should see those results soon.

Judging by where Afontova-Gora is on the autosomal PCA, Sungir should be in about the same place.

parasar
12-01-2013, 03:55 AM
I doubt any of the mammoth-steppe hunters belonged to R1a-M417. And I doubt that Z93 arrived in South Asia before the Bronze Age. But Afontova-Gora 2 almost certainly belonged to R and mtDNA U, and so did Sungir. We should see those results soon.

Judging by where Afontova-Gora is on the autosomal PCA, Sungir should be in about the same place.

When the Mal'ta boy was found to be R it was mentioned that that meant that R was present in Europe too - "they seem to have been markers of hunter-gatherer populations that roamed across the Mammoth Steppe all the way from Iberia to North America" "R looks like the best candidate for a paternal marker of the Mammoth Steppe from Iberia to Siberia."

Then when Afontova Gora 2 was thought to be M417*, you mentioned that "then Eastern Europeans at the time were also M417*"

Who else could unify such a large swath in the 24000ybp to 17000ybp than the mammoth hunters?

I'm not sure about Z93, but sure looks like that the Mal'ta R folk were from SE Asia possibly getting to the Baikal via southern India.

Generalissimo
12-01-2013, 04:23 AM
Then when Afontova Gora 2 was thought to be M417*, you mentioned that "then Eastern Europeans at the time were also M417*"

If Afontova Gora was indeed M417*, then yes, M417* was in Europe at the same time. But considering the contaminated sample and the fact that it's been sitting in a Russian museum all these years, then I doubt the M417 result is genuine. R is very likely though, when we get a more reliable sequence.


I'm not sure about Z93, but sure looks like that the Mal'ta R folk were from SE Asia possibly getting to the Baikal via southern India.

I doubt they were from anywhere near Southern India or Southeast Asia, because the Mal'ta clade shows deep differentiation with South Indians, East Asians and Oceanians. The reason for his high membership in the South Asian cluster is because that cluster is a composite of West Asian, European and South Indian allele frequencies. Pre-East Asian Siberia looks the most likely origin of the main Mal'ta clade.

http://img845.imageshack.us/img845/9195/tsg5.png

http://img811.imageshack.us/img811/4151/zubo.png

And there's no way we're going to work out where P originated or expanded from based on modern DNA.

parasar
12-01-2013, 04:41 AM
If Afontova Gora was indeed M417*, then yes, M417* was in Europe at the same time. But considering the contaminated sample and the fact that it's been sitting in a Russian museum all these years, then I doubt the M417 result is genuine. R is very likely though, when we get a more reliable sequence.



I doubt they were from anywhere near Southern India or Southeast Asia, because the Mal'ta clade shows deep differentiation with South Indians, East Asians and Oceanians. The reason for his high membership in the South Asian cluster is because that cluster is a composite of West Asian, European and South Indian allele frequencies. Pre-East Asian Siberia looks the most likely origin of the main Mal'ta clade.

And there's no way we're going to work out where P originated or expanded from based on modern DNA.

We can try. After all that's what we have doing for the last few years. Otherwise all the exercises you have been engaging in with modern DNA might as well be garbage, which it is definitely not, it just has to be calibrated with ancient DNA.

Have you looked at pre-East Asian Siberia, other than Malta and AG-2?

As far as contamination is concerned, "humerus (MA-1) from Mal'ta and a humerus (AG-2) from Afontova Gora-2 were sampled" and "Bone powder from MA-1 and AG-2 (149 mg and 119 mg ..." was drilled out from inside the humerus.

Generalissimo
12-01-2013, 05:05 AM
Have you looked at pre-East Asian Siberia, other than Malta and AG-2?

Well yeah, what about the Denisovan cave? That produced the Denisovan genome and a Neanderthal genome that looked ancestral to those in West Eurasia. So there was a lot of interesting things happening in Siberia prior to the Ice Age. It was a bit of hub, probably with nice weather, fishing and hunting.

When more mammoth-steppe genomes are sequenced they'll create a mammoth-steppe cluster, and then we'll be able to see more clearly where admixture from this population is found today. I'm betting we'll see around 60% of it across Northern Europe, peaking in the East Baltic, around 20-50% in South and South Central Asia, and probably something like 4% in modern Papuans.


As far as contamination is concerned, "humerus (MA-1) from Mal'ta and a humerus (AG-2) from Afontova Gora-2 were sampled" and "Bone powder from MA-1 and AG-2 (149 mg and 119 mg ..." was drilled out from inside the humerus.

I'm just going by what the paper says, and it says that Afontova-Gora 2 is heavily contaminated.

parasar
12-01-2013, 05:55 AM
Well yeah, what about the Denisovan cave? That produced the Denisovan genome and a Neanderthal genome that looked ancestral to those in West Eurasia. So there was a lot of interesting things happening in Siberia prior to the Ice Age. It was a bit of hub, probably with nice weather, fishing and hunting.

When more mammoth-steppe genomes are sequenced they'll create a mammoth-steppe cluster, and then we'll be able to see more clearly where admixture from this population is found today. I'm betting we'll see around 60% of it across Northern Europe, peaking in the East Baltic, around 20-50% in South and South Central Asia, and probably something like 4% in modern Papuans.



I'm just going by what the paper says, and it says that Afontova-Gora 2 is heavily contaminated.

I agree contamination is a problem:

Despite substantial present-day DNA contamination in this sample (SupplementaryInformation,section5),we findthat AG-2 shows close similarity to the genetic profile of MA-1 on a PCA (Supplemen-tary Information, section 15 and Supplementary Fig. 29) and is sig-nificantly closer to Karitiana than to Han
The Denisovan are very interesting indeed, as I think that there is a small chance they were Y-P, as it is their Y that supposedly interacted with 'modern humans.'

Bernard
12-01-2013, 07:41 AM
I asked Maanasa Raghavan about the Afontova Gora-2 mtDNA and Y-DNA tests. This is her answer:

Unfortunately, the Afontova Gora-2 sample was highly contaminated with modern DNA (as indicated in Supplementary information section 5). Hence, the only analysis we could use it for was PCA, and that too after filtering for damaged reads. By filtering for damaged reads I mean, selecting those DNA molecules which show a cytosine to thymine base change, which is characteristic of ancient DNA damage. By performing such a filtering, we can be somewhat certain that we have by and large only kept behind sequences that are ancient in origin i.e. belonging to the ancient skeleton. Such an approach of filtering was not possible for mtDNA and Y sequences because the depth of coverage (how many reads cover each base) was very low. Any filtering meant that we would lose practically all data on the mt/Y. Hence, it was not possible to determine the haplogroups for this sample.

alan
12-01-2013, 12:02 PM
I must say that what they said suggesting a unified group from Siberia to Iberia is very oversimplistic and naive in terms of archaeology. For a start most of Siberia was abandoned in the LGM. Europe was far from unified and its well known that the LGM put a major limit on movement between the east and west in Europe. There was a number of traditions and cultures like Aurignacian, Gravettian, Solutrian etc are not simplistically sequential but chronologically overlapped and hybrided too in some areas.



When the Mal'ta boy was found to be R it was mentioned that that meant that R was present in Europe too - "they seem to have been markers of hunter-gatherer populations that roamed across the Mammoth Steppe all the way from Iberia to North America" "R looks like the best candidate for a paternal marker of the Mammoth Steppe from Iberia to Siberia."

Then when Afontova Gora 2 was thought to be M417*, you mentioned that "then Eastern Europeans at the time were also M417*"

Who else could unify such a large swath in the 24000ybp to 17000ybp than the mammoth hunters?

I'm not sure about Z93, but sure looks like that the Mal'ta R folk were from SE Asia possibly getting to the Baikal via southern India.

alan
12-01-2013, 12:07 PM
Well I think that wraps it up for Afontova Gora yDNA. Nothing reliable was recovered.


I asked Maanasa Raghavan about the Afontova Gora-2 mtDNA and Y-DNA tests. This is her answer:

alan
12-01-2013, 01:21 PM
The MP thing is certainly interesting and puzzling. However, there is a lot that is unclear in origins of Palaeolithic archaeology of what was the MP period.

The south-central Siberia area of the Malta and Afontova burials seems to have been settled by early upper palaelithic groups in the 40 thousands BC, then abandoned then resettled c. 30000BC by middle upper palaeolithic groups (Mal'ta boy being a very late example of this), then abandoned again during the early LGM then resettled again by late upper palaeolithic microblade using groups c. 15000BC after the LGM. So, there are multiple human events just in Siberia. there even at a macro scale like that. I have never heard any real attempt to create a pre-Siberian origin story for the first two upper palaeolithic phases and I dont think its clear that any of them originated in Europe.

Further west, There is a bit of a shift in thinking going on anyway in the definitions of the east European upper palaeolithic with it being suggested that the term proto-Gravettian should apply to an early gravettian linked industry that passed through the Caucasus into European Russia and was far earlier than classic European Gravettian and actually co-existed with the Aurignacian in Europe.


Changing structure from K to R, is clearly pushing the origin of P-R further east.

1. Proposed by Karafet, 2008
http://2.bp.blogspot.com/_ro2ijOk8JWc/R_OzyB6YW8I/AAAAAAAAABo/1lT-OBUGV_o/s1600/ytree.jpg




2. Chiaroni K-M526, 2009 "Diamond indicates position of M526 SNP that now unifies haplogroups KMNOPS."
http://www.pnas.org/content/106/48/20174/F1.medium.gif




3. Magoon Full Genomes, 2013 X and MP

MP http://1.bp.blogspot.com/-GwlFjqHxuNk/UpPLqLlJnvI/AAAAAAAAJaM/UOjh12yl5Y8/s1600/newtree.png

alan
12-01-2013, 02:06 PM
If Sungir, Mal'ta and Afontova all belong to the same y and mt lines this will be a real eye opener as they all belong to different culture and periods. Sungir if I am not misunderstanding which sample is being tested is c. 25000BC gravettian while Mal'ta boy was 22000BC south-central Siberian middle Upper Palaeolithic culture. Most people see these as differently rooted although there are broad similarities in art etc.

Afanatova is even stranger as there is no way that his culture can be derived from Europe as the microblade technology had not even reached that area and is vastly older in Altai than in Europe. If R or part of R stayed around in Altai during the LGM, I would be tempted to look at the spread of microblade groups west, arriving very late in the Palaeolithic in Russia and beyond as some kind of way R spread into Europe. Q has been linked to this early post-LGM spread of microblade technology eastwards so it doesnt seem outlandish that R could have been involved in its spread west. Some sort of arrival of R with microblade groups from Altai and south-central Siberia would be interesting to look at in more detail.

I have already posted above a paper about its late spread west into Russia and beyond. Some think its just parallel adaption but it could be migratory and it does seem to have some kind of cline that starts around the Altai where it was probably contained throughout the LGM.


I doubt any of the mammoth-steppe hunters belonged to R1a-M417. And I doubt that Z93 arrived in South Asia before the Bronze Age. But Afontova-Gora 2 almost certainly belonged to R and mtDNA U, and so did Sungir. We should see those results soon.

Judging by where Afontova-Gora is on the autosomal PCA, Sungir should be in about the same place.

alan
12-01-2013, 04:33 PM
Afontova's autosomal results indicate that west Eurasians remained around Altai or thereabout during the LGM. I am not aware of any European palaeolithic cultures intruding into the Balkai area and that zone of Siberia in general either just before or just after the LGM. The expansion of the culture that the Afontova guy was part of was an expansion from the south of microblade groups who reoccupied the south-central Siberia area at the end of the LGM. That indicates to me that an European-like elements in the area were already in the area before the Mal'ta boy and at least a section of this chose to retreat to Altai and became the ancestors of the Afontova guy. This makes sense given the origins of the Q native Americans who have been linked as most close to some Altai clades. Clearly they went on to mix with others on their route to America through east Asia and Berningia but some of these Altains at the end of the LGM clearly went in directions if the spread of the microblade groups is any sort of guide.

parasar
12-01-2013, 04:34 PM
...

Afanatova is even stranger as there is no way that his culture can be derived from Europe as the microblade technology had not even reached that area and is vastly older in Altai than in Europe. If R or part of R stayed around in Altai during the LGM, I would be tempted to look at the spread of microblade groups west, arriving very late in the Palaeolithic in Russia and beyond as some kind of way R spread into Europe. Q has been linked to this early post-LGM spread of microblade technology eastwards so it doesnt seem outlandish that R could have been involved in its spread west. Some sort of arrival of R with microblade groups from Altai and south-central Siberia would be interesting to look at in more detail.

I have already posted above a paper about its late spread west into Russia and beyond. Some think its just parallel adaption but it could be migratory and it does seem to have some kind of cline that starts around the Altai where it was probably contained throughout the LGM.

Assuming the birth of P in SE Asia 50000 to 40000ybp, do we know why a people would move from SE Asia to Siberia in that time frame?

Jean M
12-01-2013, 04:39 PM
The Denisovan are very interesting indeed, as I think that there is a small chance they were Y-P, as it is their Y that supposedly interacted with 'modern humans.'

There is no chance at all of this.


A male child inherits its father's Y-DNA haplogroup in toto. There is no way for a male parent to insert a "foreign" SNP into a Y-DNA signature from the female parent. The female parent has no Y.
Denisovan mtDNA and Y-DNA are different from that of modern humans.
The Y-DNA tree in modern humans is constructed of a clear chain of mutations. The SNPs L138, PF5983/L268, PF5962/M45, PF5963/N12/M74 etc that define P simply distinguish that node from its ancestor K(xLT). P-carriers have all the SNPs of its ancestor K(xLT), which has all the SNPs of its ancestor K and so on back to A0-T or A0'1'2'3'4, depending on nomenclature:
http://www.isogg.org/tree/ISOGG_YDNATreeTrunk.html
http://www.yfull.com/tree/
http://www.phylotree.org/Y/tree/index.html


In short P is a descendant of A0-T or A0'1'2'3'4 (same thing).

alan
12-01-2013, 05:32 PM
Not sure. A great deal of population movements in prehistory are due to climate/ecological changes (especially how wet/dry) so I would imagine the answer is there although I have never read up on this in terms of that geographical area.

One simple reason for an eastern entry might be the lack of a good pass from Afghanistan as far as Altai and then nothing as far as Manchuria or thereabouts. That would have limited the options for movement of anyone northwards from south Asia.

I think though that while an initial southern route is suggested by an MP branch, I think there is a danger people feel this means we have to place the origin point close to where M is today. I dont think this is the case. The P branch is just as important in guessing the origin of MP. We have direct evidence of R* in Balkia area c. 22000BC and another man with autosomal DNA nearby in 15000BC who used a microblade technology probably developed in the Altain refuge c. 25000BC. We also know that that would have been the nearest refuge for the group at Mal'ta. Finally a close clade link between native Americans and south Altai has been established for haplogroup Q. Altai keeps popping up! I think given that Altai was the closest line of retreat in the LGM, it is also possible that P or R/Q could have earlier used the very same route to enter Siberia. The options are limited and Altai is one of the few without heading even farther east. The Dzungarian gate allows access between south central Siberia and SE Asia. For me, when you look for alternatives for entering Siberia from southern Asia you almost have to go as far as Iran in the west or perhaps some tricky Afghanistan crossing. NB I am not sure how the last glaciation has altered the passes that would have been available in 30-40,000BC.


Assuming the birth of P in SE Asia 50000 to 40000ybp, do we know why a people would move from SE Asia to Siberia in that time frame?

jeanL
12-01-2013, 05:40 PM
In short P is a descendant of A0-T or A0'1'2'3'4 (same thing).

But A0-T or A0'1'2'3'4 doesn't exist, is a made up term, it certainly doesn't exist in Africa, nor does it exist anywhere. :\

parasar
12-01-2013, 06:23 PM
Denisovan ...Y-DNA are different from that of modern humans.


I may be wrong, but I thought the Denisovans tested were females while the movement of their genes to human is supposed to be male biased.


The apparent lack of Denisovan alleles on the X chromosome suggested that some of these archaic interbreeding events were male biased, that is archaic males mating with modern females
http://arxiv.org/ftp/arxiv/papers/1212/1212.6820.pdf


male dominated gene infusion between Denisovan and Papuan lineages
http://arxiv.org/ftp/arxiv/papers/1112/1112.6424.pdf


Of more relevance may be examination of aspects of the Denisovan karyotype. The great apes have 24 pairs of chromosomes while humans have 23 ... Denisovans and modern humans (and presumably Neandertals) shared a karyotype consisting of 46 chromosomes.
http://genetics.med.harvard.edu/reich/Reich_Lab/Welcome_files/2012_Science_Meyer_DenisovaSeq.pdf

So in the scenario I was envisioning, the Denisovans were Y-P already in SE Asia via interaction with Y-P Papuans. When they moved to Siberia, they transferred the P there. That is one of the plausible ways P could have moved from SE Asia to Siberia to western Asia and gave an advantage to humans in west asia through associated immunity genes.


... modern humans acquired the HLA-B*73 allele in west Asia through admixture with archaic humans called Denisovans ...
Figure S6 Models for the distribution of HLA-B*73 http://www.sciencemag.org/content/suppl/2011/08/19/science.1209202.DC1/1209202-Abi-Rached.SOM.pdf

GailT
12-01-2013, 06:29 PM
But A0-T or A0'1'2'3'4 doesn't exist, is a made up term, it certainly doesn't exist in Africa, nor does it exist anywhere. :\

A0-T is a partial estimate of the NRY sequence of a man who lived around 140,000 years ago. This man was the common ancestor of all men in clades below A0-T. Obviously no living man has the same NRY sequence as did A0-T, but this is a man who did exist in Africa.

You could also claim that R1a and R1b do not exist, and that they certainly do not exist in Europe or Asia. Yet we all recognize that this is a totally meaningless statement, as we all understand that R1a and R1b refer to men who did exist in Eurasia and who were the common ancestors of R1a and R1b subclades who spread throughout Eurasia.

Jean M
12-01-2013, 06:41 PM
I may be wrong, but I thought the Denisovans tested were females.

My mistake, I should have said that the Y-DNA haplogroups of Neanderthals are different from those of modern humans, and we can have every expectation of finding exactly the same case for the Denisovans, unless the samples we obtain are from Denisovan-modern crosses, with the male parent human.

parasar
12-01-2013, 06:48 PM
...

I think though that while an initial southern route is suggested by an MP branch, I think there is a danger people feel this means we have to place the origin point close to where M is today. I dont think this is the case. The P branch is just as important in guessing the origin of MP ...

The parallel branch to MP, X-NO helps your scenario somewhat as X(NO) was recently found in a southern Indian sample. But S again is SE Asia specific, so the overall center of gravity is clearly towards S-SE Asia which looks to have sent multiple waves out: P-Q,R followed by X(NO)-N, O

Another point to note is that not only M is SE Asian, but the Papuan sample HGDP00542 has derived P locations too.

Jean M
12-01-2013, 06:56 PM
So in the scenario I was envisioning, the Denisovans were Y-P already in SE Asia via interaction with Y-P Papuans. When they moved to Siberia, they transferred the P there.

Why not cut out the archaic middle man? Why complicate the story for no reason? Occam's Razor, yes?

jeanL
12-01-2013, 07:48 PM
A0-T is a partial estimate of the NRY sequence of a man who lived around 140,000 years ago. This man was the common ancestor of all men in clades below A0-T. Obviously no living man has the same NRY sequence as did A0-T, but this is a man who did exist in Africa.


Correction: A0-T is believed to be a man who likely(Given the current phylogenetic tree) lived in Africa, but for all we know he could have lived anywhere else.

GailT
12-01-2013, 08:24 PM
Correction: A0-T is believed to be a man who likely(Given the current phylogenetic tree) lived in Africa, but for all we know he could have lived anywhere else.

Of course we have a great deal of evidence indicating that he lived in Africa, and no evidence indicating that he lived anywhere else. If you include A00, we have more than 200,000 years of the deepest branching of the y-DNA tree whose descendents are found primarily in Africa today, and almost everyone outside of Africa descends from one relatively young branch of that African tree.

Jean M
12-01-2013, 08:35 PM
There is a thread for people to argue over Out-of-Africa. Here it is: http://www.anthrogenica.com/showthread.php?1486-Did-modern-humans-come-out-of-Africa

parasar
12-01-2013, 10:44 PM
Why not cut out the archaic middle man? Why complicate the story for no reason? Occam's Razor, yes?

I agree. Direct movement of P without any Denisovan involvement is undoubtedly the simplest scenario. After all Kostenki 14 U2 was morphologically close to Papuans and Melanesians.

The morphology of his skeleton is generally quite modern. Certain cranial features, including very narrow braincase, low and narrow face, marked prognathism (anterior protrusion of the midface), and very wide nose, are typical of tropical populations. The trait combination links the cranium with those of Papuans and Melanesians.

alan
12-02-2013, 12:45 AM
I read something recently that the Early Upper Palaeolithic in Altai apparently resembles the Bohunician in that a Levallois type flint technique was used. Anyway the description of the Altai early upper palaeolithic sounds very like what I have read about the south-central Siberian early upper palaeolithic. The culture ultimately was replaced or transformed. I wonder what on earth to make of the possibilities for this? I known the Bohunician is thought to relate to anatomically modern humans because of its similarity to the Emiran culture of the near east which is associated with AMHs.

alan
12-02-2013, 02:17 AM
This paper on the early upper Palaeolithic in Altai and nearby will be free in a few days. The summary at the end can be accessed

https://openaccess.leidenuniv.nl/bitstream/handle/1887/19054/English%20Summary.pdf?sequence=33

It indicates a couple of early upper palaeolithic waves which sounds rather like the Bohunician then Aurignacian entry sequence into Europe. Neither is thought to have roots in the local Neanderthal-Mousterrain cultures although I think the first of that pair of early upper palaeolithic groups in the paper did use a levallois flint knapping technique often associated with Neanderthals as did the Bohunician in Europe (which however is thought to be linked to a culture in Levant which did belong to anatomically modern humans). Its a fascinating subject but what seems to me to a lack of consistency of terminology makes it hard to read.

Certainly, there is a lot of mystery in terms of the human groups involved. The paper suggests the most likely population sources for the early upper palaeolithic groups in Altai and nearby parts of Siberia was central Asia.

Jean M
12-02-2013, 12:10 PM
After all Kostenki 14 U2 was morphologically close to Papuans and Melanesians.

The phenotype of Kostenki 14 man simply means that his ancestors lived in the tropics (as indeed did all our ancestors if you go back far enough). Adaptation to northern climates had yet to occur. It does not mean that he was particularly closely related to any particular modern tropical population. His mtDNA is more informative about his specific origins. Do we find U2 among Papuans and Melanesians? No. It most probably arose in what I call the Asian cross-roads, with some then moving south into South Asia (where we find U2a-c) and some westwards to move across the Caucasus into Europe (where we find Ue).

newtoboard
12-02-2013, 01:03 PM
That would depend on how many matches there were with Q (if any, as I did not see Maximus report any) and how many with R(1 reported) then R1(2 reported) and then R1a1 (7 reported).
If it were modern contamination we would get many more matches, and a high number would be modern lineages downstream of Page7. We have also got remember that Genetiker found this sample to be much more European shifted than the Mal'ta one.

How did he come out autosomally?

newtoboard
12-02-2013, 01:06 PM
I doubt any of the mammoth-steppe hunters belonged to R1a-M417. And I doubt that Z93 arrived in South Asia before the Bronze Age. But Afontova-Gora 2 almost certainly belonged to R and mtDNA U, and so did Sungir. We should see those results soon.

Judging by where Afontova-Gora is on the autosomal PCA, Sungir should be in about the same place.

Yea I agree. NW Europe's R1a diversity is artificial. It has been the sink not the source for all these types of R1a.

parasar
12-02-2013, 03:31 PM
The phenotype of Kostenki 14 man simply means that his ancestors lived in the tropics (as indeed did all our ancestors if you go back far enough). Adaptation to northern climates had yet to occur. It does not mean that he was particularly closely related to any particular modern tropical population. His mtDNA is more informative about his specific origins. Do we find U2 among Papuans and Melanesians? No. It most probably arose in what I call the Asian cross-roads, with some then moving south into South Asia (where we find U2a-c) and some westwards to move across the Caucasus into Europe (where we find Ue).

The same can be said about P.
The scenario that looks the most plausible is that the transition mtDNA R->U2 and Y P->R happened in southern India where we find significant amounts of R-207 and P(xM207, xM242).

Beyond the regular tropical features of the Kostenki 14 is a prominent Australoid type deep upper nasal notch:

...
http://newsimg.bbc.co.uk/media/images/47021000/jpg/_47021484__mg_0199-1.jpg

"Balangodese ... deep nasal notch" http://books.google.com/books?id=W6zQHNavWlsC&pg=PA238

parasar
12-02-2013, 03:35 PM
How did he come out autosomally?

Autosomally AG-2 is similar to MA-1, but AG-2 is transitioning more towards European.

Jean M
12-02-2013, 04:19 PM
@ Parasar

I know that you are fascinated by the phenotype of this individual from Kostenki. You have said all this before. But it is really not all that surprising if an early Homo sapiens arrival in Europe looked a bit like an early Homo sapiens in East Africa, India, Australia, North Africa or anywhere else within the same sort of period (40-50,000 years ago), or that such a phenotype should survive in a few places in the world relatively undisturbed by the later gene sweeps that gave us the regional variety we have today.

It does not tell us anything at all about the route of arrival at Kostenki, let alone where mtDNA U2 arose. There is no support for the birth of U2 in Southern India. It arose not from R, but from U. The geographical scatter of subclades of U suggests a birth for U at a point between the Levant and South Asia, not somewhere within South Asia.

parasar
12-02-2013, 07:35 PM
@ Parasar

I know that you are fascinated by the phenotype of this individual from Kostenki. You have said all this before. But it is really not all that surprising if an early Homo sapiens arrival in Europe looked a bit like an early Homo sapiens in East Africa, India, Australia, North Africa or anywhere else within the same sort of period (40-50,000 BC), or that such a phenotype should survive in a few places in the world relatively undisturbed by the later gene sweeps that gave us the regional variety we have today.

Jean,

I have not see anyone mention a North or East Africa type phenotype for this Kostenski individual. My bet would be that over 90% would pick Vedda or Australian Aborigine, especially when you point out the characteristic nasal notch.

When I mentioned the migrations maps will need to be changed to reflect a movement out of SE Asia, you said you would wait for the consensus. Is Michael Hammer consensus enough?



It does not tell us anything at all about the route of arrival at Kostenki, let alone where mtDNA U2 arose. There is no support for the birth of U2 in Southern India. It arose not from R, but from U. The geographical scatter of subclades of U suggests a birth for U at a point between the Levant and South Asia, not somewhere within South Asia.

SE Asia harbors some of the oldest and most diverged M, N, and R lines. U2 arose somewhere on its way from SE Asia. My analysis based on current distribution tells me that that place likely is southern India which harbors all the basal nodes. While U2 is present in greater proportions in northern India, they are derivatives of southern Indian types. There is U* in southern India too.

Jean M
12-02-2013, 08:37 PM
Jean, I have not see anyone mention a North or East Africa type phenotype for this Kostenski individual.

Naturally. People in North and East Africa today do not look like Australian Aborigines. Yet Australian Aborigines descend from people who lived in East Africa long ago. It is pointless to compare a man who lived 33,000 years ago only with living people.

Perhaps you might like to look at some more reconstructions? http://kenanmalik.wordpress.com/2012/12/15/the-battle-of-the-bones/kennewick_reconstruction/

http://www.berkeley.edu/news/multimedia/2003/06/slideshow_pt1.html

Notice the deep upper nasal notch on the Herto man reconstruction.

http://ma.prehistoire.free.fr/qafzeh9.htm Qafzeh 9 skull from the Levant (https://en.wikipedia.org/wiki/Skhul_and_Qafzeh_hominids) reconstructed by Richard Neave.

http://www.kenniskennis.com/site/sculptures/Head%20reconstructions%20realistic/

parasar
12-02-2013, 10:18 PM
Naturally. People in North and East Africa today do not look like Australian Aborigines. Yet Australian Aborigines descend from people who lived in East Africa long ago. It is pointless to compare a man who lived 33,000 years ago only with living people.

Perhaps you might like to look at some more reconstructions? http://kenanmalik.wordpress.com/2012/12/15/the-battle-of-the-bones/kennewick_reconstruction/

http://www.berkeley.edu/news/multimedia/2003/06/slideshow_pt1.html

Notice the deep upper nasal notch on the Herto man reconstruction of the cranium (below).

Frankly, to me, none of these look even remotely close to the Kostenki 14 fella who looks Australoid. The Native American Kennewick barely appears 'tropical.'

The Herto man does show a notch below the forehead in the reconstruction.
http://www.berkeley.edu/news/media/releases/2003/06/images/HsapiensAdultFE_med.jpg

What I talking about though is something more defined that is seen in old crania from Europe and the Balangodese also is seen at present among the Vedda and Australian Aborigines. That Herto man is from 160ybp, while the Balangodese and Kostenki are contemporaries.

As I had mentioned on another thread I am looking for evidence between 100000 and 40000ybp, to establish the provenance of these Upper Paleolithic humans. To me, both the Balangodese and Kostenki are migrants from somewhere else, and while Africa is possible, I have yet to see any proof.

Jean M
12-02-2013, 10:28 PM
To me, both the Balangodese and Kostenki are migrants from somewhere else, and while Africa is possible, I have yet to see any proof.

I am not suggesting that the Kostenki 14 man arrived in Europe direct from Africa. No early sapiens arrived in Europe direct from Africa. The Mediterranean was an impassible barrier at the time. The only debate has been over which routes were taken via Asia. If you want to argue with Out-of-Africa, there is a thread specially for it. Let's not hijack yet another thread.

parasar
12-02-2013, 10:48 PM
I am not suggesting that the Kostenki 14 man arrived in Europe direct from Africa. No early sapiens arrived in Europe direct from Africa. The Mediterranean was an impassible barrier at the time. The only debate has been over which routes were taken via Asia. If you want to argue with Out-of-Africa, there is a thread specially for it. Let's not hijack yet another thread.

With respect to the discussion about Afontova and/or Mal'ta, I think Kostenki 14 as well as where Kostenki 14 came from is pertinent.
I did not bring up Africa as I had no reason to do so.

alan
12-03-2013, 12:47 AM
He is interesting but he comes from a different culture and phase, I believe from the pre-Gravettian Aurignoid layers of that site. So, its not clear if he is linked to the same human waves that produced the Mal'ta and Afontova guys. From an archaeological point of view they are three quite different cultures.


With respect to the discussion about Afontova and/or Mal'ta, I think Kostenki 14 as well as where Kostenki 14 came from is pertinent.
I did not bring up Africa as I had no reason to do so.

parasar
12-03-2013, 02:32 AM
Judging by where Afontova-Gora is on the autosomal PCA, Sungir should be in about the same place.

Generalissimo,

What is your opinion on Genitiker's autosomal report on Mal'ta and Afontova Gora? Are you planning to run the data and report your findings?

Thanks.

Generalissimo
12-03-2013, 02:58 AM
Generalissimo,

What is your opinion on Genitiker's autosomal report on Mal'ta and Afontova Gora? Are you planning to run the data and report your findings?

Thanks.

Maybe, but it's not easy to get the data. It needs a lot of bandwidth and some processing, which is not straightforward. So we'll see.

If Genetiker actually got the processing of the data right, then another major problem remains: fitting the ancient genomes to ancestral clusters created with populations that came into being more or less 17-24,000 years after these genomes existed. So it's like turning everything on its head, and then trying to make sense of it.

Perhaps it's better to wait until a good number of ancient high-quality genomes become available online, already processed by the top minds in the field of ancient genomics? Then we can get the ancient genomes to create ancient clusters, and fit modern samples to these clusters.

parasar
12-03-2013, 06:02 PM
Not sure. A great deal of population movements in prehistory are due to climate/ecological changes (especially how wet/dry) so I would imagine the answer is there although I have never read up on this in terms of that geographical area.
...

Perhaps the sinking of Sundaland in the 65000-50000ybp time frame forced the move. We have YTT, then an 1000year ice age, and then flooding. During this period modern humans may have survived in southern most parts of Africa and east of Toba, Flores, Australia, etc.


When the island was colonised by the Dutch in the 16th century they repeatedly heard stories of Little People having been seen in the jungle from the indigenous Homo sapiens Ngadha and Manggarai tribes, but none of these rumours appear to have been proven.
http://www.bradshawfoundation.com/homo_floresiensis.php


He is interesting but he comes from a different culture and phase, I believe from the pre-Gravettian Aurignoid layers of that site. So, its not clear if he is linked to the same human waves that produced the Mal'ta and Afontova guys. From an archaeological point of view they are three quite different cultures.

I think Kostenki 14 is one the early ones to enter Eastern Europe, Y-P or early R is my speculation. The transition would be from Kostenki 14->Mal'ta MA1 ->Afotova Gora AG2 with progression from the Australoid type to West Eurasian Caucasian.

parasar
12-04-2013, 04:16 AM
...

I had guessed to myself that Afontova would be haplogroup Q. There doesnt seem to be any R in Altai other than much later R1a that probably came from the west.

...


Sorry I am lost. They found indications of both R1a and Q? I have got to be honest that Q is what I thought the Afantova person would be based on a complex of considerations. However, they were clearly concerned about contamination or they would have provided a conclusion on the Afontova Y DNA.

AF2 None Q1a1 Q1a1a Q1a1b F1215 R http://www.yfull.com/full-genomes/

alan
12-04-2013, 12:42 PM
However his date is not very early. I believe about 30000BC. There was human settlement in that zone long before that.


Perhaps the sinking of Sundaland in the 65000-50000ybp time frame forced the move. We have YTT, then an 1000year ice age, and then flooding. During this period modern humans may have survived in southern most parts of Africa and east of Toba, Flores, Australia, etc.


http://www.bradshawfoundation.com/homo_floresiensis.php



I think Kostenki 14 is one the early ones to enter Eastern Europe, Y-P or early R is my speculation. The transition would be from Kostenki 14->Mal'ta MA1 ->Afotova Gora AG2 with progression from the Australoid type to West Eurasian Caucasian.

parasar
12-04-2013, 01:13 PM
However his date is not very early. I believe about 30000BC. There was human settlement in that zone long before that.

37985+-665

parasar
12-12-2013, 10:55 PM
AG2/YFull

R1a1 Level
M609/"M609 CTS836 R1a1a1 equivalent or upstream"
Y1429 ?
CTS11148 /"CTS11148 R1a1a1 equivalent or upstream"
PAGE7/"PAGE7 R1a1a1"
M752/"M752 PF7527 F2948 R1a1a1 equivalent or upstream"
M761/"M761 F3159 R1a1a1 equivalent or upstream"
M810/"M810 F3644 R1a1a1 equivalent or upstream"

parasar
12-29-2013, 04:05 AM
He is interesting but he comes from a different culture and phase, I believe from the pre-Gravettian Aurignoid layers of that site. So, its not clear if he is linked to the same human waves that produced the Mal'ta and Afontova guys. From an archaeological point of view they are three quite different cultures.


Mikhail Gerasimov thought that Mal'ta originated from Southeastern Asia.


Mal'ta was first excavated between 1928 and 1958 by Mikhail Mikhaylovich Gerasimov ...
http://archaeology.about.com/od/upperpaleolithic/fl/Malta-Russia.htm


M. M. Gerasimov (Institute of Ethnography, Moscow) reported on the results of his latest excavations at the important Palreolithic site of Mal'ta near Irkutsk. In his opinion, the geological, stratigraphic and faunal evidence establish this as one of the oldest sites in Siberia. The distinctive features of the stone and bone artifacts, as well as of the representational art, provide a basis for defining the 'Mal'ta culture', represented by this site and the roughly contemporary but probably slightly later site of Buret' in this same general area. As to the ancestry of the Mal'ta culture, Gerasimov finds no corroboration of Okladnikov's hypothesis of a Western (European) origin. He feels that certain elements of the flint tool inventory, as well as of the art, indicate the distinctive nature of this culture and give grounds for advancing the hypothesis of a southeastern origin
http://scholarspace.manoa.hawaii.edu/bitstream/handle/10125/16665/AP-v5n1-118-126.pdf?sequence=1

bicicleur
01-21-2014, 10:47 AM
I read something recently that the Early Upper Palaeolithic in Altai apparently resembles the Bohunician in that a Levallois type flint technique was used. Anyway the description of the Altai early upper palaeolithic sounds very like what I have read about the south-central Siberian early upper palaeolithic. The culture ultimately was replaced or transformed. I wonder what on earth to make of the possibilities for this? I known the Bohunician is thought to relate to anatomically modern humans because of its similarity to the Emiran culture of the near east which is associated with AMHs.

that is interesting Alan, do you remember where you read that?
what culture or time period of the Altai was that? was it the same period as Emiran/Bohunician (50/48000 years ago) ?

parasar
05-28-2014, 11:24 PM
http://genetiker.wordpress.com/2014/05/28/y-snp-calls-for-afontova-gora-2/
Mixed results in line with prior reports.

R.Rocca
05-28-2014, 11:38 PM
http://genetiker.wordpress.com/2014/05/28/y-snp-calls-for-afontova-gora-2/
Mixed results in line with prior reports.

While 'genetiker' states that the sample is Q1a1, couldn't the R1a result be just as valid? I guess the contamination aspect also comes into play.

lgmayka
05-29-2014, 12:13 AM
http://genetiker.wordpress.com/2014/05/28/y-snp-calls-for-afontova-gora-2/
Mixed results in line with prior reports.
Q-F1215 has definitely been found in Poland (kit 180029) and Ireland (kit 53601). (See here (http://www.semargl.me/de/dna/ydna/item-snp/4096/).) Near-matches have been found in Hungary.

parasar
05-29-2014, 01:18 AM
While 'genetiker' states that the sample is Q1a1, couldn't the R1a result be just as valid? I guess the contamination aspect also comes into play.

Yes. Actually the weight is towards some kind of R1 (R1-P245/PF6117 ... R1a Page7 ...R1b L226/S168).

ADW_1981
05-29-2014, 02:09 AM
Yes. Actually the weight is towards some kind of R1 (R1-P245/PF6117 ... R1a Page7 ...R1b L226/S168).

Somehow I'm thinking a subclade below L21 (S168) is highly unlikely....

parasar
05-29-2014, 03:21 AM
Somehow I'm thinking a subclade below L21 (S168) is highly unlikely....

Especially if this read by Centurion/Maximus of YFull is correct:


...
P
M1186
M1232
Y492
L781
Y1796
Y1611
M1256
M1264
M1252
PF5971
M1189

R
Y369

R1
PF6525
Y101

R1a1a
M609
Y1429
CTS11148
PAGE7
M752
M761
M810

http://forum.molgen.org/index.php/topic,6301.105.html

alan
05-30-2014, 09:17 PM
If I am understanding correctly that you are saying that that Q clade is incredibly rare today then the probability of its presence being modern contamination since excavation is remote, unlike R1a which there would be a high probability of Russians shedding and contaminating.


Q-F1215 has definitely been found in Poland (kit 180029) and Ireland (kit 53601). (See here (http://www.semargl.me/de/dna/ydna/item-snp/4096/).) Near-matches have been found in Hungary.

lgmayka
05-30-2014, 09:38 PM
If I am understanding correctly that you are saying that that Q clade is incredibly rare today then the probability of its presence being modern contamination since excavation is remote, unlike R1a which there would be a high probability of Russians shedding and contaminating.
Yes, but I am also saying that this particular Q clade is not utterly absurd. Rare, isolated remnants of it survive even in Europe.

venustas
06-03-2014, 01:28 AM
Afantova had haplogroup (F)Q1a1 and some type of (N)R derived mtdna.

YFULL removed the sample . However, I saved a screenshot showing evidence that Afantova had haplogroup (F)Q1a1 F1215.
Also Turkmens do not have (F)R1b they have (F)Q1a (just thought I point it out).
http://snag.gy/S1RSQ.jpg
It is high unlikely that the (F)Q1a1 is contamination as (F)Q1a1 is near non-existent in Russia, even the kets don't have this clade of (F)Q. (F)R1a1 from a Russian must have contaminated Afantova.

parasar
06-11-2014, 03:52 PM
Afantova had haplogroup (F)Q1a1 and some type of (N)R derived mtdna.

YFULL removed the sample . However, I saved a screenshot showing evidence that Afantova had haplogroup (F)Q1a1 F1215.
Also Turkmens do not have (F)R1b they have (F)Q1a (just thought I point it out).
http://snag.gy/S1RSQ.jpg
It is high unlikely that the (F)Q1a1 is contamination as (F)Q1a1 is near non-existent in Russia, even the kets don't have this clade of (F)Q. (F)R1a1 from a Russian must have contaminated Afantova.

Their initial determination was:
"AF2 Nov. 24, 2013, 4:48 p.m. None Q1a1"
http://yfull.com/news/ [now that entry is gone]

On a forum (November 24, 2013, 17:00:40), YFull's Centurion posted additional SNP's of the R1a1 type.

"Боюсь что все факты указывают на R1a1a."["I'm afraid that all the evidence points to R1a1a."] [for Afontova Gora 2]
http://forum.molgen.org/index.php/topic,6301.90.html

As the sample could not have been both R1a1 and Q1a1, poor sample quality was assumed, and therefore, both claims were withdrawn.
Semargl of Yfull, quoted previously on this thread: "He has several positive SNPs Q. The remaining SNPs of haplogroup R1a. Sample quality is very poor.
I did not want to publish data on this sample, but some people could not resist"

The reads for both R1a1 and Q1a1 were also confirmed by Genetiker. http://genetiker.wordpress.com/2014/05/28/y-snp-calls-for-afontova-gora-2/
Q1a1-F1215, R1-P245/PF6117, R1a1a1-Page7

AJL
06-11-2014, 04:24 PM
Afantova had haplogroup (F)Q1a1 and some type of (N)R derived mtdna.

YFULL removed the sample . However, I saved a screenshot showing evidence that Afantova had haplogroup (F)Q1a1 F1215.
Also Turkmens do not have (F)R1b they have (F)Q1a (just thought I point it out).
http://snag.gy/S1RSQ.jpg
It is high unlikely that the (F)Q1a1 is contamination as (F)Q1a1 is near non-existent in Russia, even the kets don't have this clade of (F)Q. (F)R1a1 from a Russian must have contaminated Afantova.

Is there some reason you keep posting "F"s in front of actual haplogroups? I don't think anybody knows what you mean by that. F is its own haplogroup.

ADW_1981
06-11-2014, 04:46 PM
Is there some reason you keep posting "F"s in front of actual haplogroups? I don't think anybody knows what you mean by that. F is its own haplogroup.

I've noticed many users are trying to correlate features in modern populations based on a very ancient node splits such as those who split from YDNA F, and I've seen this fairly extensively on YDNA P recently, and the relationship between Q and R for example. What people are not realizing is that these splits occurred many 10's of thousands of years ago and often have nothing to do with physical features or even geography, especially when trying to determine whether the R1 male was Central Asian or SE Asian. (for example)

venustas
06-12-2014, 05:12 AM
Is there some reason you keep posting "F"s in front of actual haplogroups? I don't think anybody knows what you mean by that. F is its own haplogroup.

No I was just saying R is a subclade of F. If everyone in E has an E in front of them shouldn't everyone in F, since E and F have similar diversity?

AJL
06-12-2014, 05:15 PM
No I was just saying R is a subclade of F. If everyone in E has an E in front of them shouldn't everyone in F, since E and F have similar diversity?

That's not how it works.

venustas
06-12-2014, 07:58 PM
That's not how it works.

Its just nomenclature. Seriously though if you belong to y-dna F you belong to y-dna F and it should be noted in your haplogroup.
Nowadays, F (G+H+I+J+K+L+T+M+N+O+P+Q+R) y-dna is the dominant y-dna in the globe, however in a few hundred years that may no longer be the case. No matter how dominant the haplogroup, the subclades should not be given new names. The current y-dna nomenclature is unscientific, and instead of renaming the entire thing why not just put the name of the macro haplogroup in front?

AJL
06-12-2014, 08:08 PM
instead of renaming the entire thing why not just put the name of the macro haplogroup in front?

Because according to that logic you would have to name R-P312, say, not "R-P312" but

A00 - A0-T - BT - CT - CF - F - GHIJK - HIJK - K - P - R - R1 - R1b - R1b1 - R1b1a - R1b1a2 - R1b1a2a - R1b1a2a1 - R1b1a2a1a - R1b1a2a1a2


which is cumbersome, redundant, and imbecilic, and contrary to the entire point of using a phylogenetic tree.

venustas
06-13-2014, 12:31 AM
good point.