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Dr_McNinja
11-18-2014, 08:35 PM
You are closest to BR2 and Ust-Ishim.

Ust-Ishim is essentially ancestral ASI so that looks in line.

BR2 is Y-J2a1b so perhaps there is come connection via the common J2 ancestry.

At 4cM and above I have no matches except Ust Ishim indicating more ancestral ASI and less basal:
4/400
Chr Start Location End Location Centimorgans (cM) SNPs
1 202903493 206135760 4.3 619
20 56621015 58868193 8.2 565
21 34819638 36731307 4.8 450
Largest segment = 8.2 cM
Total of segments > 4 cM = 17.4 cM

5/500
Chr Start Location End Location Centimorgans (cM) SNPs
20 56621015 58868193 8.2 565
Largest segment = 8.2 cM
Total of segments > 5 cM = 8.2 cM

How close is Ust-Ishim to ASI? Could we use it in Admixture tests?

parasar
11-18-2014, 08:57 PM
How close is Ust-Ishim to ASI? Could we use it in Admixture tests?

Quite close, I suppose.
Ancestral ASI split from basal 2000 generations back. ~50000 years at 25yr/gen.
Ancestral ASI split into ASI, ‘proto-East Asia’ and ancestors of Onge 1700 generations back. ~42500 years at 25yr/gen
Ust-Ishim's date falls between the two, so yes Ust-Ishim chould be a good proxy for ASI.

Ebizur
11-19-2014, 09:53 PM
Ancestral ASI split from basal 2000 generations back. ~50000 years at 25yr/gen.On what grounds have you made this estimate? 50,000 YBP should be quite close to the era of the MRCA of the well-known subclades of F-M89 (GHIJK).


Ancestral ASI split into ASI, ‘proto-East Asia’ and ancestors of Onge 1700 generations back. ~42500 years at 25yr/gen
Ust-Ishim's date falls between the two, so yes Ust-Ishim chould be a good proxy for ASI.42,500 YBP should be close to the era of the MRCA of N-M231 and O-M175 or the MRCA of P1-M45 and P*-P295(xM45).

parasar
11-19-2014, 10:30 PM
On what grounds have you made this estimate? 50,000 YBP should be quite close to the era of the MRCA of the well-known subclades of F-M89 (GHIJK).

42,500 YBP should be close to the era of the MRCA of N-M231 and O-M175 or the MRCA of P1-M45 and P*-P295(xM45).

They are based on my interpretation of Reich et. al.'s numbers from their ANI/ASI paper. pg 40 http://www.nature.com/nature/journal/v461/n7263/extref/nature08365-s1.pdf
"2,000 gens (Europe-Asia split)" or "Split of ANI and ASI ancestors" which in my interpretation is ASI splitting from basal European, and I see it supported based on which side of the split Ust-Ishim lies.

Followed by "1,700 gens (Asian split)" or "Split of Asian populations (‘proto-East Asia’, ASI, and Onge)"

Reich's paper also indicated in a way the time-frame of ANE entering from the ancestral ASI side into the ancestral ANI side I think when they say "600 gens ago Gene flow from ‘proto-East Asia’ into the ancestral population of ANI and West Eurasians" which comes to 15000ybp and in light of 24000 year old MA1 is quite possible.

Overall while these are depicted as discreet events, in reality they are likely composites of multiple events.

That whole M89 to M9 to M526 is quite close, so yes 50000ybp looks quite possibly time-wise the point of a major split.

Ebizur
11-19-2014, 11:20 PM
They are based on my interpretation of Reich et. al.'s numbers from their ANI/ASI paper. pg 40 http://www.nature.com/nature/journal/v461/n7263/extref/nature08365-s1.pdf
"2,000 gens (Europe-Asia split)" or "Split of ANI and ASI ancestors" which in my interpretation is ASI splitting from basal European, and I see it supported based on which side of the split Ust-Ishim lies.

Followed by "1,700 gens (Asian split)" or "Split of Asian populations (‘proto-East Asia’, ASI, and Onge)"

Reich's paper also indicated in a way the time-frame of ANE entering from the ancestral ASI side into the ancestral ANI side I think when they say "600 gens ago Gene flow from ‘proto-East Asia’ into the ancestral population of ANI and West Eurasians" which comes to 15000ybp and in light of 24000 year old MA1 is quite possible.

Overall while these are depicted as discreet events, in reality they are likely composites of multiple events.

That whole M89 to M9 to M526 is quite close, so yes 50000ybp looks quite possibly time-wise the point of a major split.
But then what might modern examples of C-M130 and DE-YAP represent? They should be even more "basal" than "Basal Eurasian" in such a scenario.

Note that the TMRCA ([C+F]+DE) and the TMRCA of (C+F) are very ancient; TMRCA ([C+F]+DE) - TMRCA (G+HIJK) or TMRCA (C+F) - TMRCA (G+HIJK) should be approximately equal to TMRCA ([C+F]+DE) * (1/3) or TMRCA (C+F) * (1/3), which should be approximately equal to 25,000 years assuming that TMRCA (G+HIJK) is 50,000 years. TMRCA ([C+F]+DE) or TMRCA (C+F) should be about 75,000 years. The TMRCA (B + CFDE) should be about 107,000 years, so another 32,000 years or so before the MRCA of CFDE. Most parsimoniously, the OoA migration should have occurred some time between 107,000 YBP and 75,000 YBP.

parasar
11-19-2014, 11:50 PM
But then what might modern examples of C-M130 and DE-YAP represent? They should be even more "basal" than "Basal Eurasian" in such a scenario.

Note that the TMRCA ([C+F]+DE) and the TMRCA of (C+F) are very ancient; TMRCA ([C+F]+DE) - TMRCA (G+HIJK) or TMRCA (C+F) - TMRCA (G+HIJK) should be approximately equal to TMRCA ([C+F]+DE) * (1/3) or TMRCA (C+F) * (1/3), which should be approximately equal to 25,000 years assuming that TMRCA (G+HIJK) is 50,000 years. TMRCA ([C+F]+DE) or TMRCA (C+F) should be about 75,000 years. The TMRCA (B + CFDE) should be about 107,000 years, so another 32,000 years or so before the MRCA of CFDE. Most parsimoniously, the OoA migration should have occurred some time between 107,000 YBP and 75,000 YBP.
I see CDEF as the OoA split.
They come before the ASI split. That OoA split I belive Reich calculated as 4000 generations back. Essentially they would be in the background of both ANI and ASI ancestors.

Ebizur
11-20-2014, 02:57 AM
I see CDEF as the OoA split.Do you mean that you agree with my position that the Out-of-Africa migration most likely has occurred at some time after the MRCA of (B + CFDE) and before the MRCA of (CF + DE), i.e. some time between approximately 107,000 YBP and approximately 75,000 YBP?


They come before the ASI split. That OoA split I belive Reich calculated as 4000 generations back. Essentially they would be in the background of both ANI and ASI ancestors.If the "2,000 gens (Europe-Asia split)" or "Split of ANI and ASI ancestors" really does correspond to a split between ASI(?=Ust-Ishim-like proto-"Crown Eurasians") and basal European(="Basal Eurasian") as you have suggested, and this split has occurred roughly 50,000 YBP (around the time of the derivation of G, H, I, J, and K), then the age of the split between Eurasians and Africans caused by the Out-of-Africa migration of proto-Eurasians should be roughly twice that age (i.e. approximately 100,000 YBP), correct? A split between Eurasians and Africans dating to approximately 100,000 YBP should be not long after the genealogical split between CT-M168 and B-M60, which I have estimated to be approximately 107,000 YBP.

However, the Y-DNA of a majority of modern Africans belongs to clades downstream of CT-M168. Some of their mtDNA (certainly the M and N derivatives, but also possibly some clades traditionally classified as subclades of L3(xM, N) that are often positioned by tree-building algorithms as basal branches of the M clade: cf. Lippold et al. 2014, Fu et al. 2014, etc.) may also be associated with a migration or migrations from Eurasia to Africa subsequent to the Out-of-Africa migration of proto-Eurasians. Is Reich's estimate of the time of the split between proto-Eurasians and their relatives left behind in Africa insensitive to such subsequent Eurasian → African admixture?

parasar
11-20-2014, 04:37 AM
Do you mean that you agree with my position that the Out-of-Africa migration most likely has occurred at some time after the MRCA of (B + CFDE) and before the MRCA of (CF + DE), i.e. some time between approximately 107,000 YBP and approximately 75,000 YBP?


Yes. I think the split is a little earlier so I would go with the upper end of the range.



If the "2,000 gens (Europe-Asia split)" or "Split of ANI and ASI ancestors" really does correspond to a split between ASI(?=Ust-Ishim-like proto-"Crown Eurasians") and basal European(="Basal Eurasian") as you have suggested, and this split has occurred roughly 50,000 YBP (around the time of the derivation of G, H, I, J, and K), then the age of the split between Eurasians and Africans caused by the Out-of-Africa migration of proto-Eurasians should be roughly twice that age (i.e. approximately 100,000 YBP), correct? A split between Eurasians and Africans dating to approximately 100,000 YBP should be not long after the genealogical split between CT-M168 and B-M60, which I have estimated to be approximately 107,000 YBP.

However, the Y-DNA of a majority of modern Africans belongs to clades downstream of CT-M168. Some of their mtDNA (certainly the M and N derivatives, but also possibly some clades traditionally classified as subclades of L3(xM, N) that are often positioned by tree-building algorithms as basal branches of the M clade: cf. Lippold et al. 2014, Fu et al. 2014, etc.) may also be associated with a migration or migrations from Eurasia to Africa subsequent to the Out-of-Africa migration of proto-Eurasians. Is Reich's estimate of the time of the split between proto-Eurasians and their relatives left behind in Africa insensitive to such subsequent Eurasian → African admixture?

E is IMO a back migration to Africa. CF, YAP almost spring out together, within the margin of error of SNP counting backwards from the present, say +- 750 years. So I think either both were African, or E is a back migration. Based on current distribution, it appears that the latter is more likely.

I would say that Reich's date for the split from autosomal calculations is not that sensitive to a Y line, but there should be some evidence from the basal European side going back to Africa (perhaps via mainly E).

Ebizur
11-20-2014, 06:38 AM
E is IMO a back migration to Africa. CF, YAP almost spring out together, within the margin of error of SNP counting backwards from the present, say +- 750 years. So I think either both were African, or E is a back migration. Based on current distribution, it appears that the latter is more likely.I generally agree with what you have written here, but I would consider three lineages (C, F, and YAP+) rather than two because the connection between C and F as opposed to YAP+ is fleeting if not tenuous.


I would say that Reich's date for the split from autosomal calculations is not that sensitive to a Y line, but there should be some evidence from the basal European side going back to Africa (perhaps via mainly E).I understand the reasons for such a hypothesis, but it seems curious to me that of the haplogroups often suspected of indicating a very old migration from Eurasia to Africa, all but one are more closely related to haplogroups typical of certain modern East Asian and Andamanese populations (Y-DNA DE(xE), mtDNA M) than to anything else. The only exception is mtDNA haplogroup U6, which is related to the mtDNA of every published Palaeolithic Eurasian AMH as far as I know (to the mtDNA of the Kostenki 14 specimen from the Don watershed and the later Mal'ta specimen from the vicinity of Lake Baikal at the level of haplogroup U and to the mtDNA of the Ust'-Ishim specimen from the Ob-Irtysh watershed and the Tianyuan specimen from northern China at the level of haplogroup R). If this hypothetical early Eurasian influence in Africa has been mediated mostly by "Basal Eurasian" (in your terms, "Basal European") populations, it seems that such populations must have shared some haploid similarity with an early population of East Asia that is not reflected in the haploid gene pools of "Western Eurasian" populations derived from the "Crown Eurasian" node. Would you explain this as a result of ancient East Asians' being basal to the "Crown Eurasian" node (or, in other words, "Crown Eurasian" having derived from an early population of AMHs in East Asia)?

parasar
11-20-2014, 03:40 PM
I generally agree with what you have written here, but I would consider three lineages (C, F, and YAP+) rather than two because the connection between C and F as opposed to YAP+ is fleeting if not tenuous.

Breaking up CF into C, F is fine as that split is also almost contemporaneous. I think ancient DNA will show them not as opposed as we are lead to believe from modern distribution though.



I understand the reasons for such a hypothesis, but it seems curious to me that of the haplogroups often suspected of indicating a very old migration from Eurasia to Africa, all but one are more closely related to haplogroups typical of certain modern East Asian and Andamanese populations (Y-DNA DE(xE), mtDNA M) than to anything else. The only exception is mtDNA haplogroup U6, which is related to the mtDNA of every published Palaeolithic Eurasian AMH as far as I know (to the mtDNA of the Kostenki 14 specimen from the Don watershed and the later Mal'ta specimen from the vicinity of Lake Baikal at the level of haplogroup U and to the mtDNA of the Ust'-Ishim specimen from the Ob-Irtysh watershed and the Tianyuan specimen from northern China at the level of haplogroup R). If this hypothetical early Eurasian influence in Africa has been mediated mostly by "Basal Eurasian" (in your terms, "Basal European") populations, it seems that such populations must have shared some haploid similarity with an early population of East Asia that is not reflected in the haploid gene pools of "Western Eurasian" populations derived from the "Crown Eurasian" node. Would you explain this as a result of ancient East Asians' being basal to the "Crown Eurasian" node (or, in other words, "Crown Eurasian" having derived from an early population of AMHs in East Asia)?

I see it quite possible that ~100000 to 50000ybp East Asians could be 'basal' to "Crown Eurasian" but I admit I don't fully understand the concept of basal. I would appreciate if someone could clarify the concept.

The main reason I consider basal Eurasian to be basal European is that it has been discerned from European ancient DNA. It may actually have been present in West Asia and North Africa too.

Reich group's San paper was interesting as they IMO were seeing basal European deep in Africa. To emphasize basal European and not basal Eurasian.

Pickrell et. al.:
http://www.pnas.org/content/111/7/2632.full


The largest amplitudes are obtained with European populations as references (Fig. 1A); taken literally, this would seem to implicate Europe as the source of admixture (although Middle Eastern populations are also among the best proxies).


Analysis:
http://www.newscientist.com/article/dn24988-humanitys-forgotten-return-to-africa-revealed-in-dna.html#.VG4IwDTF8xE


Back to Africa – but from where?
Reich and his colleagues found that DNA sequences in the Khoisan people most closely resemble some found in people who today live in southern Europe. That, however, does not mean the migration back to Africa started in Italy or Spain. More likely, the migration began in what is now the Middle East.

We know that southern Europeans can trace their ancestry to the Middle East. However, in the thousands of years since they – and the ancestors of the Khoisan – left the region, it has experienced several waves of immigration. These waves have had a significant effect on the genes of people living in the Middle East today, and means southern Europeans are much closer to the original inhabitants of the Levant than modern-day Middle Easterners.

everest59
11-20-2014, 05:41 PM
Basal Eurasian as Reich used it is essentially basal West Eurasian because East Asians don't have it. So I agree with your definition of basal Eurasian as it should be basal to everybody. Ust Ishim is in reality basal Eurasian.
Basically speaking, basal Eurasian as Reich used it is a component that shows affinity to African populations. It essentially lowers shared drift calculation numbers because the software confuses it with African.
I would say E probably originated in Africa because Europeans have more of this basal component than the Yorubas have Asian or West Asian.
In reality basal Eurasian should be basal to all Eurasians but that's not how Reich's lab used the term.

everest59
11-20-2014, 05:42 PM
Btw, how common is E in South Asia?

parasar
11-20-2014, 06:06 PM
Btw, how common is E in South Asia?

Trace to absent across South Asia. It is present in migrants from West Asia and Africa though.
There was one E reported in a Dungri Bheel and a YAP in a Koraga sample.
http://www.academia.edu/221582/Yap_Insertion_signature_in_south_Asia

bored
11-20-2014, 06:26 PM
Btw, how common is E in South Asia?

According to Wiki, E1b1b is present at a frequency of 8 % among the Baloch.
http://en.wikipedia.org/wiki/Y-DNA_haplogroups_by_ethnic_group

parasar
11-20-2014, 08:42 PM
The eastern Tharus also have it in the 8% range:
http://1.bp.blogspot.com/_Ish7688voT0/Sk9-TO7DceI/AAAAAAAABwY/9QUGqTOlQfA/s1600/tharus.jpg



Abhik et. al. had found some E1b types in Bangladesh, but I can't locate the paper.
Genotyping Bengali males from Bangladesh and the West Bengal Indian state



See also post by Ebizur:

The E-P1 in Laran is really the most perplexing of all, in my opinion, because it cannot be explained by influence from East Asia, Indochina, or South Asia.

http://www.anthrogenica.com/showthread.php?2957-New-Study-on-y-dna-and-mtdna-frequencies-in-West-Timor-Kakaniuk-has-25-5-P-y-dna&p=47739&viewfull=1#post47739

everest59
11-20-2014, 08:53 PM
Interesting that only one group has it among 6.
Btw, has Sri Lankan 1000 genomes ydna data been published yet? How about Bengalis or Punjabis?

parasar
11-20-2014, 09:14 PM
Interesting that only one group has it among 6.
Btw, has Sri Lankan 1000 genomes ydna data been published yet? How about Bengalis or Punjabis?

Coincidentally that same group has elevated J2a and J2b.
I have seen E pop up in both Bengalis and Punjabis.

Do you mean the STU dataset? If so, they should be here: http://biorxiv.org/content/biorxiv/suppl/2013/12/13/000802.DC5/000802-3.pdf

bored
11-20-2014, 11:40 PM
Interesting that only one group has it among 6.
Btw, has Sri Lankan 1000 genomes ydna data been published yet? How about Bengalis or Punjabis?

Do you think it's reasonable to assume that Baloch types have the highest Basal Eurasian in South Asia? I mean given how West shifted they are, it seems to make sense.

everest59
11-20-2014, 11:50 PM
Do you think it's reasonable to assume that Baloch types have the highest Basal Eurasian in South Asia? I mean given how West shifted they are, it seems to make sense.

Yup, the Baloch must have the highest basal Eurasian in South Asia.

bored
11-21-2014, 12:04 AM
Yup, the Baloch must have the highest basal Eurasian in South Asia.

Thanks. Do you know how much Basal Eurasian there is in Gedrosian type EEF, since that is the main type of EEF present in South Asians? As per Lazaridis et al, it makes up about 44 % of EEF but that percentage might be different for South Asia specific EEF. Intuitively it seems like it should be lower because South Asia is much further from Africa and does not have much Y-DNA E presence.

Dr_McNinja
11-21-2014, 12:09 AM
Thanks. Do you know how much Basal Eurasian there is in Gedrosian type EEF, since that is the main type of EEF present in South Asians? As per Lazaridis et al, it makes up about 44 % of EEF but that percentage might be different for South Asia specific EEF. Intuitively it seems like it should be lower because South Asia is much further from Africa and does not have much Y-DNA E presence.Gedrosian type ENF gets split by Admixture from Bedouin-type ENF in South Asians. The latter is usually higher (it's the Caucasian plus half the "South Indian" plus actual Near East components whereas Gedrosian-type ENF in Baloch tops out around 20-30%... the other Bedouin-type is averaging 29-31% across South Asia, almost mirroring ANE in its distribution but peaking more in South/West India).

I'm not even sure if Gedrosian was a real ancestral population. It could just be due to extreme genetic drift. Lower k shows it to be a sister component to the Caucasus. So whether it matches a specific population movement event in time is still unknown. And it doesn't necessarily have to have come from the Caucasus either. Maybe they branched off coming out of the Near East on their way to the Caucasus...

EDIT: This could be one map of movement: http://i.imgur.com/j61XECg.png Probably shouldn't have put East Asian in there though since that's a different timeframe. We don't know if ANE input into Gedrosian/Baloch happened in or near South Central Asia either. It could be that the ENF wave out of the Near East went into India and straight north where it mixed with ANE and then came back down in successive waves, and one of the later waves brought some East Eurasian too. This would be in line with the idea that Gedrosian represents a real population movement event whereas the picture assumes it doesn't.

everest59
11-21-2014, 12:12 AM
Thanks. Do you know how much Basal Eurasian there is in Gedrosian type EEF, since that is the main type of EEF present in South Asians? As per Lazaridis et al, it makes up about 44 % of EEF but that percentage might be different for South Asia specific EEF. Intuitively it seems like it should be lower because South Asia is much further from Africa and does not have much Y-DNA E presence.

That's really hard to calculate. Basal Eurasian can't even be calculated for current European populations. Otherwise Lazaridis would have reported it.
I tried to calculate it once, a long time ago. It simply does not work on current populations. I got 70-80% basal Eurasian in all populations(European or West Asian or South Asian), which was essentially speaking crap.

everest59
11-21-2014, 12:14 AM
Gedrosian type ENF gets split by Admixture from Bedouin-type ENF in South Asians. The latter is usually higher (it's the Caucasian plus half the "South Indian" plus actual Near East components whereas Gedrosian-type ENF in Baloch tops out around 20-30%... the other Bedouin-type is averaging 29-31% across South Asia, almost mirroring ANE in its distribution but peaking more in South/West India).

I'm not even sure if Gedrosian was a real ancestral population. It could just be due to extreme genetic drift. Lower k shows it to be a sister component to the Caucasus. So whether it matches a specific population movement event in time is still unknown. And it doesn't necessarily have to have come from the Caucasus either. Maybe they branched off coming out of the Near East on their way to the Caucasus...

Yeah, I think it's just drift.

bored
11-21-2014, 12:22 AM
Gedrosian type ENF gets split by Admixture from Bedouin-type ENF in South Asians. The latter is usually higher (it's the Caucasian plus half the "South Indian" plus actual Near East components whereas Gedrosian-type ENF in Baloch tops out around 20-30%... the other Bedouin-type is averaging 29-31% across South Asia, almost mirroring ANE in its distribution but peaking more in South/West India).

I'm not even sure if Gedrosian was a real ancestral population. It could just be due to extreme genetic drift. Lower k shows it to be a sister component to the Caucasus. So whether it matches a specific population movement event in time is still unknown. And it doesn't necessarily have to have come from the Caucasus either. Maybe they branched off coming out of the Near East on their way to the Caucasus...

Good point. It's probably drift. I think most EEF everywhere is rather Bedouin like. In places where it got to thousands of years ago that are far away from the source, it went through some genetic drift making it register differently on calculators. EEF has been present in South Asia for thousands of years so you'd expect that's enough time for portions of it to undergo a lot of genetic drift even before any mixing events with ASI and ANE.
If you think about it, Sardinians aren't all that different from Bedouins.

redifflal
11-21-2014, 01:09 AM
Hasn't Balochi society integrated East African slaves and soldiers in the last 1000 years? I understand there are separate Sheedi/Makrani communities, but the larger Balochis aren't following some one drop rule I'm guessing. I always wondered about using Balochis as a proxy for South Asian genetics for this reason.

Megalophias
11-21-2014, 07:23 AM
Basal Eurasian as Reich used it is essentially basal West Eurasian because East Asians don't have it. So I agree with your definition of basal Eurasian as it should be basal to everybody.
It IS basal to everybody. Basal means it branched off before the split of East and West Eurasians (the "pure" form of the latter being WHG). Your cousin is basal to you and your brothers and sisters, for example, because you are all more closely related to each other than to your cousin. So it isn't just basal to Europeans - that would mean it branched off before Europeans but after East Asians, which is not the case. It doesn't matter that Basal Eurasians didn't subsequently admix into East Eurasians, they are still basal to them. (Of course this is all hypothetical since we don't have any actual Basal Eurasians, but assuming they did exist.)



Hasn't Balochi society integrated East African slaves and soldiers in the last 1000 years? I understand there are separate Sheedi/Makrani communities, but the larger Balochis aren't following some one drop rule I'm guessing. I always wondered about using Balochis as a proxy for South Asian genetics for this reason.

From what I understand (which could be completely wrong), the Balochi incorporate other people quite readily; according to their own (Islamic) legends, they come from Syria; their language is classified as Northwestern Iranian, and probably arrived from further west in the Middle Ages; and a large number of them (the Brahui) speak a Dravidian language (almost always bilingually), and probably come from the southern half of India. So yeah, it's a safe bet that they are quite mixed.

aarnisotka
11-21-2014, 10:09 AM
It IS basal to everybody. Basal means it branched off before the split of East and West Eurasians (the "pure" form of the latter being WHG). Your cousin is basal to you and your brothers and sisters, for example, because you are all more closely related to each other than to your cousin. So it isn't just basal to Europeans - that would mean it branched off before Europeans but after East Asians, which is not the case. It doesn't matter that Basal Eurasians didn't subsequently admix into East Eurasians, they are still basal to them. (Of course this is all hypothetical since we don't have any actual Basal Eurasians, but assuming they did exist.)




From what I understand (which could be completely wrong), the Balochi incorporate other people quite readily; according to their own (Islamic) legends, they come from Syria; their language is classified as Northwestern Iranian, and probably arrived from further west in the Middle Ages; and a large number of them (the Brahui) speak a Dravidian language (almost always bilingually), and probably come from the southern half of India. So yeah, it's a safe bet that they are quite mixed.

It is basal in the sense that it represents, the first split between OOAs. But 'Basal Eurasian' can not be seen to represent basal eurasians if they have after the initial split acquired slight extra affinity to Africa. In fact the closest genetic descendants of the original OOAs in that model are East Eurasians. So East Asians are the Basal Eurasians.

Lets say BE does not have African admixture. Even in that model it would not be basal to East Asians as both lack admixtures from each other, thus they would be equally basal. Just two branches of the original dudes.

Jean M
11-21-2014, 11:01 AM
It is basal in the sense that it represents, the first split between OOAs. But 'Basal Eurasian' can not be seen to represent basal eurasians if they have after the initial split acquired slight extra affinity to Africa.

There seems to be a confusion here between modern and ancient DNA. In the Lazaridis paper 'Basal Eurasian' was a label for a 'ghost' ancient population of which we do not yet have an ancient representative. It was deduced from its presence in EEF to have been in the Near East in the Neolithic. It does not make any difference if some of this population entered Africa after splitting from the original Out-of-Africa migration.

There also seems to be a confusion over the term 'basal' which Megalophias has clarified. A lot of people have assumed that it means 'the population from which all Eurasians descend', when in fact it represents an early split in that population, with one group (the basal) going off into such isolation from the rest that it does not contribute to all subsequent Eurasians, only some of them.

'Ancestral Eurasian' would be a good term for the ancestral group from which all Eurasians descend, but it is now looking like we have two waves out of Africa, which rather confuses the matter.

everest59
11-21-2014, 12:03 PM
It is not necessarily basal to everybody, especially if it represents a later arrival from Africa
For all I know, the later migrants had different genetics. Also, basal Eurasian does have affinity to subsaharan African and it is a higher affinity than all other ancestral Eurasian types.I am thinkinig a much later arrival for basal Eurasian.

Jean M
11-21-2014, 01:07 PM
It is not necessarily basal to everybody, especially if it represents a later arrival from Africa.

It does not. Lazaridis makes it absolutely clear that 'Basal Eurasian' is not a subsequent arrival from Sub-Saharan Africa. It split away from the group that had left Africa. If you think of it as the autosomal equivalent to Y-DNA E, it might help to visualise it. Africa today is full of E. It spread with farmers to almost obliterate the more ancient Y-DNA haplogroups of Africa, A and B, associated with hunter-gatherers.

Basal does not mean ancestral, as Megalophias explained. 'Basal Eurasian" does not equal "Ancestral Eurasian." In other words "Basal Eurasian" does not mean the OOA ancestral group. "Basal Eurasian" is a group that split away from the OOA ancestral group. The OOA ancestral group = Ancestral Eurasian = the ancestors of all people native to the world outside Africa.

What complicates matters is that lots of people living in Africa today also have DNA that descends from the OOA group.

parasar
11-21-2014, 01:39 PM
It does not. Lazaridis makes it absolutely clear that 'Basal Eurasian' is not a subsequent arrival from Sub-Saharan Africa. It split away from the group that had left Africa. If you think of it as the autosomal equivalent to Y-DNA E, it might help to visualise it. Africa today is full of E. It spread with farmers to almost obliterate the more ancient Y-DNA haplogroups of Africa, A and B, associated with hunter-gatherers.

Basal does not mean ancestral, as Megalophias explained. 'Basal Eurasian" does not equal "Ancestral Eurasian." In other words "Basal Eurasian" does not mean the OOA ancestral group. "Basal Eurasian" is a group that split away from the OOA ancestral group. The OOA ancestral group = Ancestral Eurasian = the ancestors of all people native to the world outside Africa.

What complicates matters is that lots of people living in Africa today also have DNA that descends from the OOA group.

So folk on each side of the split are basal to each other.
If your cousin is basal to you and your siblings, you are basal to your cousin and your cousin's siblings.
Africans are a population basal to all Eurasians.

everest59
11-21-2014, 01:49 PM
It does not. Lazaridis makes it absolutely clear that 'Basal Eurasian' is not a subsequent arrival from Sub-Saharan Africa. It split away from the group that had left Africa. If you think of it as the autosomal equivalent to Y-DNA E, it might help to visualise it. Africa today is full of E. It spread with farmers to almost obliterate the more ancient Y-DNA haplogroups of Africa, A and B, associated with hunter-gatherers.

Basal does not mean ancestral, as Megalophias explained. 'Basal Eurasian" does not equal "Ancestral Eurasian." In other words "Basal Eurasian" does not mean the OOA ancestral group. "Basal Eurasian" is a group that split away from the OOA ancestral group. The OOA ancestral group = Ancestral Eurasian = the ancestors of all people native to the world outside Africa.

What complicates matters is that lots of people living in Africa today also have DNA that descends from the OOA group.

E spreading from Asia is not a done deal.
Then explain why basal Eurasian shows more affinity to African than do other Eurasians. Other people can run the softwares and verify it themselves. If it is an ooa split we should all be quite distant from modern Africans. But so is not the case due to the fact that basal Eurasian just like African reduces shared drift f3 scores.

parasar
11-21-2014, 01:57 PM
E spreading from Asia is not a done deal.
Then explain why basal Eurasian shows more affinity to African than do other Eurasians. Other people can run the softwares and verify it themselves. If it is an ooa split we should all be quite distant from modern Africans. But so is not the case due to the fact that basal Eurasian just like African reduces shared drift f3 scores.

The so called basal is showing a little more affinity to African since southern Europe had some continued contact with Africa.
Please see Reich group's San paper referenced earlier in this thread. Post 10.

everest59
11-21-2014, 02:17 PM
The so called basal is showing a little more affinity to African since southern Europe had some continued contact with Africa.
Please see Reich group's San paper referenced earlier in this thread. Post 10.

I think you are right and it is the most plausible scenario . Stuttgart probably had some recent African ancestry.
Assuming this is the case, I would agree with basal Eurasian being an early split from ooa. The actual basal Eurasian won't have any recent African. The lazaridis basal numbers would be a mix.

bored
11-21-2014, 03:15 PM
It IS basal to everybody. Basal means it branched off before the split of East and West Eurasians (the "pure" form of the latter being WHG). Your cousin is basal to you and your brothers and sisters, for example, because you are all more closely related to each other than to your cousin. So it isn't just basal to Europeans - that would mean it branched off before Europeans but after East Asians, which is not the case. It doesn't matter that Basal Eurasians didn't subsequently admix into East Eurasians, they are still basal to them. (Of course this is all hypothetical since we don't have any actual Basal Eurasians, but assuming they did exist.)




From what I understand (which could be completely wrong), the Balochi incorporate other people quite readily; according to their own (Islamic) legends, they come from Syria; their language is classified as Northwestern Iranian, and probably arrived from further west in the Middle Ages; and a large number of them (the Brahui) speak a Dravidian language (almost always bilingually), and probably come from the southern half of India. So yeah, it's a safe bet that they are quite mixed.

Brahui did not come from South India. IMO it's not plausible. If you look at the genetic data, Brahui actually have even more of the Baloch component than the Baloch themselves. Also, they are even more West shifted than the Baloch. How could that be if they were recent migrants from Southern India?
It's possible that Brahui simply adopted a Dravidian language for various reasons. Maybe they are closer to the "original" Dravidian populations of South Asia. Perhaps most of the original Dravidian speakers migrated deep into South India except for the Brahui.

Jean M
11-21-2014, 03:20 PM
Africans are a population basal to all Eurasians.

I think you mean ancestral, but in either case, only if we are talking about ancient Africans before the departure of the OOA group(s). Africa did not float off to some inaccessible place after the OOA groups left. ;) As far as I can see, people kept coming and going between Africa and Asia from the Palaeolithic onwards. So there is Eurasian DNA in modern Africans. There is even some in the modern Koisan, whom geneticists have often used as a proxy for the ancestors of the OOA group. http://www.pnas.org/content/111/7/2632

parasar
11-21-2014, 04:09 PM
I think you mean ancestral, but in either case, only if we are talking about ancient Africans before the departure of the OOA group(s). Africa did not float off to some inaccessible place after the OOA groups left. ;) As far as I can see, people kept coming and going between Africa and Asia from the Palaeolithic onwards. So there is Eurasian DNA in modern Africans. There is even some in the modern Koisan, whom geneticists have often used as a proxy for the ancestors of the OOA group. http://www.pnas.org/content/111/7/2632

No I don't.
For example, if you see Lazaridis' tree, the Mbuti are not ancestral but basal to all non-Africans. Ancestors of Mbuti and non-Africans are no longer extant. Downstream of the split both sides are basal to each other.
I agree that exchange could be diffuse, but for the model discrete events are assumed.

http://3.bp.blogspot.com/-YbYK8NzQNAY/UrihRsR5eSI/AAAAAAAAJbo/TYynaV4cO4Y/s1600/model.png

Jean M
11-21-2014, 04:30 PM
For example, if you see the Lazaridis' tree, the Mbuti are not ancestral but basal to all non-Africans. Ancestors of Mbuti and non-Africans are no longer extant.

I follow you now, but I think we really need to bear in mind that the model simplifies.

Jean M
11-21-2014, 07:31 PM
Then explain why basal Eurasian shows more affinity to African than do other Eurasians.

I already have done. Africa is full of people partly descended from farmers from the Near East. Farmers can out-breed foragers. This is what happened in Europe. This is what happened in Africa. A lot of the descendants of early farmers in Africa are carrying Y-DNA E. Some descendants of EEF farmers are carrying Y-DNA E.


E spreading from Asia is not a done deal.
Wherever Y-DNA E was actually born does not matter. It descends from DE which is a branch under CT, which seems to be the key group of OOA. So E is descended from the OOA group.

Picture a scene in which a few people descended from the OOA group mill around in Saudi Arabia and then wander back into East Africa, who have descendants millennia later who move into the Levant as the Holocene greens the Sahara. They take to farming as it moves south into the Levant. Then comes a climate crisis and so their descendants look for other places to farm. Mainly they go south into North Africa, as that is nearest. From there it filters slowly south.

R.Rocca
11-21-2014, 08:04 PM
No I don't.
For example, if you see Lazaridis' tree, the Mbuti are not ancestral but basal to all non-Africans. Ancestors of Mbuti and non-Africans are no longer extant. Downstream of the split both sides are basal to each other.
I agree that exchange could be diffuse, but for the model discrete events are assumed.

http://3.bp.blogspot.com/-YbYK8NzQNAY/UrihRsR5eSI/AAAAAAAAJbo/TYynaV4cO4Y/s1600/model.png

When I see Lazaridis' tree, I don't see the Mbuti as ancestral nor basal to all non-Africans, but rather that they both derive from one common ancestral group.

everest59
11-21-2014, 08:40 PM
I already have done. Africa is full of people partly descended from farmers from the Near East. Farmers can out-breed foragers. This is what happened in Europe. This is what happened in Africa. A lot of the descendants of early farmers in Africa are carrying Y-DNA E. Some descendants of EEF farmers are carrying Y-DNA E.


Wherever Y-DNA E was actually born does not matter. It descends from DE which is a branch under CT, which seems to be the key group of OOA. So E is descended from the OOA group.

Picture a scene in which a few people descended from the OOA group mill around in Saudi Arabia and then wander back into East Africa, who have descendants millennia later who move into the Levant as the Holocene greens the Sahara. They take to farming as it moves south into the Levant. Then comes a climate crisis and so their descendants look for other places to farm. Mainly they go south into North Africa, as that is nearest. From there it filters slowly south.

Well, unless Wikipedia is wrong, CT originated in Africa and there is a possibility that DE originated in Africa. If A and B are the only indigenous African haplogroups, what happened to the original CT or descendants? It all died out leaving no descendants behind? Now, D is obviously Asian, but there is a possibility that DE originated in Africa, and left behind E in the original CT homeland, meaning East Africa.
CT has two branches: CF and DE. If CF is Asian and DE is also Asian, then only A and B are native African? I find that very hard to believe.
What I am saying is, sure, CT is the ooa group, but there is a chance that E stayed in Africa for a while and a later second wave of E carriers spread that haplogroup around.
Supposedly E arose 50k years ago. CT almost 70k years ago per Wikipedia. That's a difference of 20k years, which is enough time to change one's genetic profile.
Come to think of it, even Chechens had their shared drift numbers reduced. Which means this is not just a Southern European thing.

Jean M
11-21-2014, 09:14 PM
Well, unless Wikipedia is wrong, originated in Africa and there is a possibility that DE originated in Africa.

It is the genetics that matter here, rather than the geography. The native modern haplogroups of Eurasia and the Americas descend from CT. So CT was the OOA signature, or at least the one which has surviving descendants. The CT group in modern people will be labelled Eurasian and American, regardless of where on the globe CT was born. They won't be labelled African.

Obviously CT descends from BT, so it is a brother of the African B. So it is quite likely that CT was born somewhere in East Africa. But that need not mean that it has direct descendants there today, other than those who represent a return to Africa. The point is this - E is an offshoot of the OOA group, as 'Basal Eurasian' is an offshoot of the OOA group.


then only A and B are native African? I find that very hard to believe.

I was absolutely staggered when it first struck me. It won't be easily accepted, I feel sure. People are still reeling in shock to find that R1a and R1b are not Palaeolithic in Europe.

parasar
11-21-2014, 09:52 PM
then only A and B are native African? I find that very hard to believe.

I was absolutely staggered when it first struck me. It won't be easily accepted, I feel sure. People are still reeling in shock to find that R1a and R1b are not Palaeolithic in Europe.

We have to remember that A, even though it occupies just one alphabet, has immense diversity.
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3113241/

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3113241/bin/gr1.jpg

lgmayka
11-22-2014, 01:19 AM
Well, unless Wikipedia is wrong, CT originated in Africa and there is a possibility that DE originated in Africa.
I have not seen any strong evidence that CT began in Africa. In fact, if one accepts Dienekes' Out Of Arabia (After Africa) hypothesis (http://dienekes.blogspot.com/2014/09/an-archaeological-scenario-for-out-of.html), even BT may have begun on the Arabian Peninsula rather than in Africa itself. The yDNA B Project (https://www.familytreedna.com/public/BYDNA/default.aspx?section=yresults) has plenty of members on the Arabian Peninsula.

Wikipedia's map of CT (http://en.wikipedia.org/wiki/Haplogroup_CT#mediaviewer/File:CT_(DECF).png) shows it beginning on the Arabian Peninsula.

In all cases I am referring to MRCAs, so the "beginning" of a macrohaplogroup is actually the point (in time and space) of its first split into subclades.

Ebizur
11-22-2014, 02:08 AM
We have to remember that A, even though it occupies just one alphabet, has immense diversity.
Furthermore, it is important to keep in mind that "haplogroup A" is a misnomer because it is not a monophyletic clade (unless one defines "haplogroup A" as "a clade to which all extant human Y-DNA belongs," which is so broad that it is rather meaningless).


I have not seen any strong evidence that CT began in Africa. In fact, if one accepts Dienekes' Out Of Arabia (After Africa) hypothesis (http://dienekes.blogspot.com/2014/09/an-archaeological-scenario-for-out-of.html), even BT may have begun on the Arabian Peninsula rather than in Africa itself. The yDNA B Project (https://www.familytreedna.com/public/BYDNA/default.aspx?section=yresults) has plenty of members on the Arabian Peninsula.

Wikipedia's map of CT (http://en.wikipedia.org/wiki/Haplogroup_CT#mediaviewer/File:CT_(DECF).png) shows it beginning on the Arabian Peninsula.

In all cases I am referring to MRCAs, so the "beginning" of a macrohaplogroup is actually the point (in time and space) of its first split into subclades.The MRCA of B and CT is much older (according to my most recent estimate calibrated on the published estimate of the time of deposition of the Ust-Ishim specimen, approximately 32,000 years older) than the MRCA of all extant CT (i.e. CF + DE). We do not have evidence from which we can draw a robust inference of the location of members of pre- or proto-CT during that span of 32,000 years. However, parasar has said that Reich et al. have estimated an autosomal split between Africans and non-Africans at about 100,000 YBP, which should be roughly around the time of the genealogical split between the lineage leading to B ("pre-B") and the lineage leading to CT ("pre-CT"). In my opinion, this should tend to support a hypothesis of pre-B having remained in Africa while pre-CT has migrated to Eurasia.

However, considering all the subsequent genetic exchanges that seem to have occurred between Eurasians and Africans after the primary split, I wonder whether that estimate of a 100,000 YBP autosomal split between Africans and non-Africans might be an underestimate. If it were so, then your idea of an "Out-of-Eurasia (Southwest Asia?)" origin of BT might be plausible.

Ebizur
11-23-2014, 12:00 AM
A couple more observations regarding the woefully neglected haplogroup B and Y*(xBT):

*At least one very early split within haplogroup B is attested in extant human Y-DNA. For example, the lineage of HGDP00931 (a B1-M236 Yoruba from Nigeria) has diverged from the lineage leading to haplogroup B2 approximately 97,000 YBP, or only about 10,000 years after the MRCA of (B+CT). TMRCA (B2a+B2b), which should represent nearly all extant members of another subclade of B (i.e. haplogroup B2-M182) that includes the Y-DNA of a great percentage of the males of Biaka, Mbuti, San, etc., is about 70,000 years, or slightly younger than the MRCA of (CF+DE). So, here we have evidence of an early split within haplogroup B, with representatives of both descendant branches being found mainly in modern Sub-Saharan African populations. Although I would not follow some people's habit of frivolously calling this "strong" evidence, it should tend to support an African localization of BT prior to a migration of pre- or proto-CT to Eurasia considering the fact that Y*(xBT) is also found mainly in Sub-Saharan African populations. However, we cannot know for certain without ancient DNA whether one or the other (or even both) of these two ancient subclades of haplogroup B has been present somewhere in Eurasia around the time of a hypothetical migration of pre- or proto-E from Eurasia to Africa.

*Haplogroup BT shares a MRCA with haplogroup A1b1-L419/PF712 (represented by at least HGDP00987 and HGDP01029, which are the genomes of two A1b1a1a-M6/M49 San from Namibia, HGDP01036, which is the genome of an A1b1b2a-M51 San from Namibia, and HGDP01406, which is the genome of an A1b1b2b-M63 Bantu speaker from Kenya) approximately 141,000 YBP. This leaves an interval of roughly 34,500 years during which pre- or proto-BT may have migrated from Africa to Asia according to your "BT Out-of-Eurasia" hypothesis under the assumption that the MRCA of BT-M91 and A1b1-L419/PF712 has been located in Africa.

everest59
11-23-2014, 03:50 PM
I have not seen any strong evidence that CT began in Africa. In fact, if one accepts Dienekes' Out Of Arabia (After Africa) hypothesis (http://dienekes.blogspot.com/2014/09/an-archaeological-scenario-for-out-of.html), even BT may have begun on the Arabian Peninsula rather than in Africa itself. The yDNA B Project (https://www.familytreedna.com/public/BYDNA/default.aspx?section=yresults) has plenty of members on the Arabian Peninsula.

Wikipedia's map of CT (http://en.wikipedia.org/wiki/Haplogroup_CT#mediaviewer/File:CT_(DECF).png) shows it beginning on the Arabian Peninsula.

In all cases I am referring to MRCAs, so the "beginning" of a macrohaplogroup is actually the point (in time and space) of its first split into subclades.

Well, but the thing here is, Arabs have African admixture. Bedouins for example can score even >10% African if you look at ADMIXTURE data.
You can see that the project has a lot of members from Saudi Arabia, which has one of the highest African admixture in that part of the world. Morocco and Tunisia do not surprise me either.

Perhaps ancient DNA will shed some light. You won't know unless we get a lot of samples. One or two won't do. That's why I am not sure if MA-1 or ancestral North Eurasian even left any descendents today (his Y-DNA is a different branch of R for example). Now, in Europe, we have a lot of data, and so we know that I is the native haplogroup, with G involved in neolithic expansion. But people really need to ask, how much can we know from one sample (MA-1)? So people have to really wonder if ANE is even real. Not just that, I notice that a lot of populations in the Caucasus have yDNA I, so one has to wonder if they really can be modeled as a simple mix of EEF and ANE.


It is the genetics that matter here, rather than the geography. The native modern haplogroups of Eurasia and the Americas descend from CT. So CT was the OOA signature, or at least the one which has surviving descendants. The CT group in modern people will be labelled Eurasian and American, regardless of where on the globe CT was born. They won't be labelled African.

I don't think CT should be seen as just Eurasian and American without more data. Some descendents of CT (e.g. CF) sure!

parasar
11-23-2014, 04:48 PM
... You won't know unless we get a lot of samples. One or two won't do. That's why I am not sure if MA-1 or ancestral North Eurasian even left any descendents today (his Y-DNA is a different branch of R for example). Now, in Europe, we have a lot of data, and so we know that I is the native haplogroup, with G involved in neolithic expansion. But people really need to ask, how much can we know from one sample (MA-1)? So people have to really wonder if ANE is even real.
...


We are not going to get many samples from that period from humid tropical zones. We will have to rely on cold, temperate and dry tropical areas. As far as ANE goes, we have some lower quality support from AG2 which is 7000 later in time and has different but related Y and mtDNA types.

everest59
11-23-2014, 04:59 PM
We are not going to get many samples from that period from humid tropical zones. We will have to rely on cold, temperate and dry tropical areas. As far as ANE goes, we have some lower quality support from AG2 which is 7000 later in time and has different but related Y and mtDNA types.

Kostenki 14 already is Europeanlike 36k years ago, and has all the components that modern Europeans do. Yet, MA-1 (who lived 14k years after) is not admixed with Stuttgart and WHG. Similarly, Loschbour is a pure WHG sample according to the authors. Something doesn't fit here, namely K14 being very Europeanlike 36K years ago. Honestly, the mistake here that the authors are making is trying to deduce ancestry based on 3-4 samples.
I feel that we are in the early stages of using ancient DNA samples to study population genetics. 10 years from now, the picture is going to be very different.

parasar
11-23-2014, 06:18 PM
Kostenki 14 already is Europeanlike 36k years ago, and has all the components that modern Europeans do. Yet, MA-1 (who lived 14k years after) is not admixed with Stuttgart and WHG. Similarly, Loschbour is a pure WHG sample according to the authors. Something doesn't fit here, namely K14 being very Europeanlike 36K years ago. Honestly, the mistake here that the authors are making is trying to deduce ancestry based on 3-4 samples.
I feel that we are in the early stages of using ancient DNA samples to study population genetics. 10 years from now, the picture is going to be very different.

True, K14 has all components in general terms. But if you note he does not have the Amerindian component that MA1 shows. Essentially I think ANE and especially WHG are just later developments of ancestral ASI of the Ust-Ishim type that did not mix with basal European while the K14 type did. In this scenario a (larger) part of K14 is from the Ust-Ishim type and a portion from the basal European Aurignacians. There is indeed an Aurignacian layer at Kostenki 14. The sample tested is from just above the CI tephra.

What I find most interesting is there is also a layer apparently below the Aurignacian which could imply that the Ust-Ishim type was present there even earlier than the Aurignacian.
http://archaeology.about.com/od/kterms/qt/Kostenki.htm

Controversy: Late Early Upper Paleolithic at Kostenki
In 2007, the excavators at Kostenki (Anikovich et al.) reported that they had identified occupation levels within and below the ash level. They found the remnants of the Early Upper Paleolithic culture called the "Aurignacian Dufour," numerous small bladelets quite similar to lithic tools found in similarly dated sites in western Europe....

At Kostenki, a sophisticated tool kit of prismatic blades, burins, bone antler, and ivory artifacts, and small perforated shell ornaments lies below the CI Tephra and Aurignacian Dufour assemblage: these were identified as an earlier presence of modern humans in Eurasia than previously recognized.
The discovery of modern human cultural material below the tephra was quite controversial at the time it was reported, and a debate about the context and date of the tephra arose. That debate was a complex one, best addressed elsewhere.

Read more about the Pre-Aurignacian deposits at Kostenki
Comments from John Hoffecker concerning initial criticism of the age of the site
Since 2007, additional sites such as Byzovaya and Mamontovaya Kurya have lent additional support to the presence of early modern human occupations of the eastern Plains of Russia.

lgmayka
11-23-2014, 08:35 PM
Well, but the thing here is, Arabs have African admixture. Bedouins for example can score even >10% African if you look at ADMIXTURE data.
One could argue that such "admixture" is precisely a signal of the Out-Of-Arabia expansion. According to this hypothesis, Bedouins do not have African admixture; rather, Africans have Arab admixture. In yDNA terms, B migrated west and southwest back into Africa, while CT headed north and northwest into Eurasia. (Or if one shifts the timeframe, E went back to Africa while CF and D colonized Eurasia.)

parasar
11-23-2014, 08:53 PM
One could argue that such "admixture" is precisely a signal of the Out-Of-Arabia expansion. According to this hypothesis, Bedouins do not have African admixture; rather, Africans have Arab admixture. In yDNA terms, B migrated west and southwest back into Africa, while CT headed north and northwest into Eurasia. (Or if one shifts the timeframe, E went back to Africa while CF and D colonized Eurasia.)

It is also possible that that African is a recent signal.
Prior to the Arab expansion S. Arabia was under east African Aksumite rule for a period of perhaps 400 years or more.

Ebizur
11-23-2014, 09:58 PM
One could argue that such "admixture" is precisely a signal of the Out-Of-Arabia expansion. According to this hypothesis, Bedouins do not have African admixture; rather, Africans have Arab admixture. In yDNA terms, B migrated west and southwest back into Africa, while CT headed north and northwest into Eurasia. (Or if one shifts the timeframe, E went back to Africa while CF and D colonized Eurasia.)The genealogical divergence of B and CT is approximately 107,000 YBP; the genealogical divergence of C, F, and DE is approximately 75,000 YBP.

Is a hypothesis that AMH have moved northward or northwestward from Arabia during that time frame plausible? Based on Fu et al. (2014), the date of Neanderthal introgression into the ancestors of the Ust'-Ishim specimen should be in the range of 59,880 YBP ~ 50,210 YBP, or roughly some time between 50,000 and 60,000 YBP. That should be somewhat later than the genealogical divergence of C, F, and DE. Because the Ust'-Ishim specimen is the oldest attestation of a genome of an anatomically modern human that contains autosomal segments that are suspected of having introgressed from Neanderthals, and the Ust'-Ishim specimen's Y-DNA belongs to haplogroup K2a (pre-XNO) and his mtDNA belongs to haplogroup R, it should be parsimonious to assume that the episode of Neanderthal introgression that has influenced the Ust'-Ishim specimen's genome has occurred through intermixture between some Neanderthal population and an AMH population that has carried pre- or proto-F Y-DNA and some early subclade of haplogroup R mtDNA (haplogroup R probably has originated prior to 60,000 YBP, whereas haplogroup K2a almost certainly has not, and the direct patrilineal ancestor of the Ust'-Ishim specimen should have been pre- or proto-F at the time of admixture between some of his ancestors and Neanderthals).

Of course, we cannot know how long it might have taken for AMH and Neanderthals to begin admixing after their ranges had begun to overlap, so the 50,000 ~ 60,000 YBP estimate of Neanderthal admixture in the population of the Ust'-Ishim specimen's ancestors is not incompatible with a northward or northwestward expansion of AMHs bearing pre- or proto-F Y-DNA at any time between approximately 75,000 YBP and approximately 50,000 YBP. The question is, do we have any physical remains of AMHs in an area north or northwest of Arabia in the period between 75,000 and 50,000 YBP that might substantiate your hypothesis? It would be wonderful if someone could extract DNA from such a skeleton and test whether it belongs to Y-DNA F (or pre-F) and mtDNA R (or pre-R).

parasar
11-24-2014, 01:12 AM
That the basal European to ASI cline is essentially the ANI-ASI extending towards Europe is clearly seen in Metspalu's PCA, with the Sardinians at the basal European end.
http://www.ncbi.nlm.nih.gov/pubmed/22152676
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3234374/bin/gr2.jpg

everest59
11-24-2014, 02:50 AM
True, K14 has all components in general terms. But if you note he does not have the Amerindian component that MA1 shows. Essentially I think ANE and especially WHG are just later developments of ancestral ASI of the Ust-Ishim type that did not mix with basal European while the K14 type did. In this scenario a (larger) part of K14 is from the Ust-Ishim type and a portion from the basal European Aurignacians. There is indeed an Aurignacian layer at Kostenki 14. The sample tested is from just above the CI tephra.

What I find most interesting is there is also a layer apparently below the Aurignacian which could imply that the Ust-Ishim type was present there even earlier than the Aurignacian.
http://archaeology.about.com/od/kterms/qt/Kostenki.htm

Keep in mind that MA-1 does not show any Siberian with Harappa (K=16), even though it should be one his more important components besides South Asian, Amerindian and Northern Euro. The point here is just because K14 does not show any Amerindian does not mean he has no relationship with MA-1.
Also, if you look at figure S24 and S25 of the supplementary materials, what you will notice is that K14 seems to form a branch with MA-1 in treemix analyses:
http://www.sciencemag.org/content/suppl/2014/11/05/science.aaa0114.DC1/Seguin-Orlando.SM.pdf

So in my opinion, there is a relationship between K14 and MA-1.
Also, why do you think MA-1 avoided mixing with K14? There needs to be a reason for it. WHG avoided mixing with basal eurasian as well?

everest59
11-24-2014, 03:14 AM
One could argue that such "admixture" is precisely a signal of the Out-Of-Arabia expansion. According to this hypothesis, Bedouins do not have African admixture; rather, Africans have Arab admixture. In yDNA terms, B migrated west and southwest back into Africa, while CT headed north and northwest into Eurasia. (Or if one shifts the timeframe, E went back to Africa while CF and D colonized Eurasia.)

I feel that these softwares do a better job of picking up more recent ancestry than they do ancient admixture. So the "African" they pick up in my opinion is recent African ancestry. To give you an example, ADMIXTURE just cannot separate out ASI from ANI properly since we are talking about a more ancient mix. What you are talking about is even more ancient. African populations tend to almost score 100% African at higher K. Now, at lower K, West Asian ancestry can show up even in the Yoruba, but Bedouins still score African.

parasar
11-24-2014, 03:34 AM
Keep in mind that MA-1 does not show any Siberian with Harappa (K=16), even though it should be one his more important components besides South Asian, Amerindian and Northern Euro. The point here is just because K14 does not show any Amerindian does not mean he has no relationship with MA-1.
Also, if you look at figure S24 and S25 of the supplementary materials, what you will notice is that K14 seems to form a branch with MA-1 in treemix analyses:
http://www.sciencemag.org/content/suppl/2014/11/05/science.aaa0114.DC1/Seguin-Orlando.SM.pdf

So in my opinion, there is a relationship between K14 and MA-1.
Also, why do you think MA-1 avoided mixing with K14? There needs to be a reason for it. WHG avoided mixing with basal eurasian as well?

MA1 and K14 clearly look to be related. My point was that K14's ancestors went west and came into contact with basal European while MA1's ancestors did not. IMO while it does look that WHG bypassed basal European on their way west, there was contact as we see from Stuttgart. Contacts are rarely one-way, but they can predominantly biased one way.

Hando
12-02-2014, 04:57 PM
I already have done. Africa is full of people partly descended from farmers from the Near East. Farmers can out-breed foragers. This is what happened in Europe. This is what happened in Africa. A lot of the descendants of early farmers in Africa are carrying Y-DNA E. Some descendants of EEF farmers are carrying Y-DNA E.


Wherever Y-DNA E was actually born does not matter. It descends from DE which is a branch under CT, which seems to be the key group of OOA. So E is descended from the OOA group.

Picture a scene in which a few people descended from the OOA group mill around in Saudi Arabia and then wander back into East Africa, who have descendants millennia later who move into the Levant as the Holocene greens the Sahara. They take to farming as it moves south into the Levant. Then comes a climate crisis and so their descendants look for other places to farm. Mainly they go south into North Africa, as that is nearest. From there it filters slowly south.
But didn't some of this same Basal Eurasian go to Europe with the first farmers to form EEF?

Neo
01-18-2015, 12:14 AM
Shriner et al. is not contemplating the Basal component which is an earlier split- earlier than 45000ybp. At 45000ybp we have Ust-Ishim who is also close to ancestral ASI as you can get, but is still almost equally close to East Asians and to the non Basal portion Europeans, Mid Easterners, and South Asians.

In general , there are pretty much no Europeans who would have Basal Eurasian components. Some Middle East Levanties would have an affinity to Basael Eurasian because these Levantine populations have been impacted by different migrations of Bedouins who carrry Arabian ACs. But Basal Eurasian can't be dated to 45,000 years in my honest opinion. If Basael Eurasian did date so far back,one would see this archaeic AC in many Out of African migrations , like those of the Ocenians,South Asians and East Eurasians. One doesn't see old mixture in MA1 or other ancient genomes. I think the reason Basal Eurasian was found in Stuggart was because it was likely brought there by a later population coming from the Arabian peninsula traversing to the Levant to East Mediterranean then To Europe. Basal Eurasian represents a younger population than the OOA-1 and OOA-2. Marc Haber et al , may have Arabians and Levantines diverging from each other at later dates but Haber does state Levantine AC and Arabian AC to have diverged from each other like Shriner, but the time is around 23kya-15kya (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3585000/). Shriner dates the split around 31kya.

The reason why Ust-Ishim would probably have East Eurasian affinities is because populations were smaller which lessened the likelihood of LD,the occurence homogeneity and less split dispersal from populations back then.

Generalissimo
01-18-2015, 03:50 AM
In general , there are pretty much no Europeans who would have Basal Eurasian components.

You're not making any sense.

Neo
01-18-2015, 08:18 AM
You're not making any sense.

Name present day European populations that exhibit traces of Basal Eurasian? The Basal Eurasian AC seems to be a cluster that hovers around Arabian peninsula and the Horn of Africa.There is only aDNA in Europe that have traces of Basal Eurasian not modern day European populations.








http://i59.tinypic.com/32zi5ok.jpg



To explore the role of the Horn of Africa in early population history and the emergence of Basal Eurasians, this month’s Digest article examines the Horn of Africa’s links with world population structure using autosomal SNP and STR data.


For each non-local component expressed in the Horn of Africa, a sequential analysis was performed by excluding that component (for instance, Nilotic in Table 1) and the next largest related component (for instance, West African in Table 2). This was repeated until no new components were identified that were related to that group (for instance, Sub-Saharan African regions in Table 2).

If we use the Lazaridis model,the only Eurasian that has strong affinities to Basal Eurasian are ''Arabians''.





A smaller percentage is expressed for only one geographically Eurasian region: Arabian (31.4%)




Basal Eurasian itself seems more associated with Afircan populations rather than Arabian populations(Eurasians),iterations have been run used for clusters of Horner African,Nilotics,West Africans, and Arabians.When the Horner AC is removed from the runs, Nilotic and West African show more relation to Basal Eurasian.




Step 1 (Remove Horn of Africa): The initial admixture analysis of the Horn of Africa excludes thelocal Horn of Africa component, expressing instead Nilotic (52.3%), Arabian (31.4%), North African(14.9%), and Khoisan-Aka (1.4%) percentages (see Table 1):





This sequential analysis indicates that the Sub-Saharan African genetic component in the Horn of Africa that is best expressed as Nilotic (see Step 1) can instead be expressed as West African (36.1%) and Khoisan-Aka (7.9%) percentages (Step 2A), or as a larger percentage of the Khoisan-Aka component (31.2%; Step 2B).



A majority of these percentages are expressed for geographically African regions (total 68.6%), possibly in part related to early African populations of modern Homo sapiens (represented by present day Mbuti in the Lazaridis tree model; see Figure 1). A smaller percentage is expressed for only one geographically Eurasian region: Arabian (31.4%). This might reflect early Non-Africanpopulations in the Lazaridis tree model (see discussion earlier in article)

Generalissimo
01-18-2015, 09:16 AM
Name present day European populations that exhibit traces of Basal Eurasian?

All present-day Europeans carry more than just traces of Basal Eurasian. That's why in comparison Mesolithic Europeans appear clearly shifted closer to East Asians.

At this point you don't have a clue what you're talking about.

Neo
01-18-2015, 09:29 AM
All present-day Europeans carry more than just traces of Basal Eurasian. That's why in comparison Mesolithic Europeans appear clearly shifted closer to East Asians.

At this point you don't have a clue what you're talking about.

Thats false.We are not talking about which populations stream towards each other we are talking about which Europeans have Basal Eurasian components. As a matter of fact Mesolithic Europeans carry more WHG-UHG admixture,with varied amounts of ANE.Post any peer reviewed where it discusses the amounts of Basal Eurasian in Europeans, I haven't seen it. In any case this study above (http://www.dnatribes.com/dnatribes-digest-2014-03-01.pdf) trumps your opinion about Basal Eurasian.

bored
01-18-2015, 09:29 AM
All present-day Europeans carry more than just traces of Basal Eurasian. That's why in comparison Mesolithic Europeans appear clearly shifted closer to East Asians.

At this point you don't have a clue what you're talking about.

Basal Eurasian makes Europeans less Eurasian like and shifted closer to Africans?

Generalissimo
01-18-2015, 10:02 AM
Post any peer reviewed where it discusses the amounts of Basal Eurasian in Europeans, I haven't seen it. In any case this study above (http://www.dnatribes.com/dnatribes-digest-2014-03-01.pdf) trumps your opinion about Basal Eurasian.

The DNA Tribes PDF doesn't prove that Europeans don't have Basal Eurasian admixture. Lazaridis et al. clearly states that all Europeans carry Stuttgart related ancestry, and Stuttgart is ~44% Basal Eurasian, so all Europeans carry Basal Eurasian admixture. That's actually a very important part of the model in that study. I have no idea how you missed it?

There are two other studies saying basically the same thing. Seguin-Orlando et al. (http://www.sciencemag.org/content/early/2014/11/05/science.aaa0114) and Qiaomei Fu et al. (http://www.nature.com/nature/journal/v514/n7523/full/nature13810.html)

You can think what you like though. The reason I'm posting here is to tell anyone else reading this that you don't have a clue what you're talking about.


Basal Eurasian makes Europeans less Eurasian like and shifted closer to Africans?

It can look like that on TreeMix graphs, but in theory what's happening is that Europeans are being pulled back towards the point from where the earliest Eurasians moved out into Eurasia and became WHG, ANE and ENA (ie. East Asians).

Neo
01-18-2015, 11:26 AM
The DNA Tribes PDF doesn't prove that Europeans don't have Basal Eurasian admixture. Lazaridis et al. clearly states that all Europeans carry Stuttgart related ancestry, and Stuttgart is ~44% Basal Eurasian, so all Europeans carry Basal Eurasian admixture. That's actually a very important part of the model in that study. I have no idea how you missed it?

There are two other studies saying basically the same thing. Seguin-Orlando et al. (http://www.sciencemag.org/content/early/2014/11/05/science.aaa0114) and Qiaomei Fu et al. (http://www.nature.com/nature/journal/v514/n7523/full/nature13810.html)

You can think what you like though. The reason I'm posting here is to tell anyone else reading this that you don't have a clue what you're talking about.



It can look like that on TreeMix graphs, but in theory what's happening is that Europeans are being pulled back towards the point from where the earliest Eurasians moved out into Eurasia and became WHG, ANE and ENA (ie. East Asians).
Post the passages in this study to back what you claim.I suspect, the studies you cite, do not say Europeans carry Stuttgart admixture in its entieriety. You're misreading the information ,the studies say that Stuttgart has ancinet genomic components that Europeans carry such WHG-UHG and ANE. Not that all Europeans today have components from Stuttgart.Besides, Stuttgart is actually considered an outlier group from the ancient genomic samples in Europe,since others don't carry Basal Eurasian.Can you comprehend that?

The WHG,UHG,EEF and ANE are ancient genomic components of what was found in the likes of ancient European samples like Loschbour, Motala12 ,La Brana, Stuttgart and others. As of the current EEF is replaced by ENF because EEF was a hybrid component made of Basal Eurasian and ANE. DNA Tribes conducts further analysis of Lazaridis et al model of Basal Eurasian admixture,in which the study basically summarizes that Basal Eurasian affinity to Horner,Nilotic and Arabian populations.Furthermore; Northern Europeans ,French/West Europeans, Central Europeans(Czech,Hungarian, etc) and even Eastern Europeans, stream closer to WHG and ANE. The modern European populations are repulsed a slight bit towards the EEF.EEF streams more closer with isolated and outler European populations such as Basques,Sardnians,and Cypriots. ENF in its unfiltered form of EEF streams towards Caucsus populations.Which one can conclude that most of ENF is a Caucasus derived component.Like I said professional scientific reviews trump yours opinions.


http://3.bp.blogspot.com/-fc2W-6tR-HA/Urigqts3hwI/AAAAAAAAJbg/hqZiV1TOGgc/s1600/europe.png

Jean M
01-18-2015, 11:57 AM
professional scientific reviews trump your opinions.

DNA Tribes does not provide professional scientific reviews. It produces laughably incompetent newsletters for its unfortunate clients, who have already been ripped off by actually paying good money for a test that cannot tell them anything like the claims made for it. See http://www.anthrogenica.com/showthread.php?3212-Why-I-do-not-recommend-DNA-tribes I wouldn't bother to read their attempts to guess the meaning of the paper by Lazaridis et al. Generalissimo is actually citing the latter paper.

This is in any case a digression from the topic of this thread. There are other threads where the heated question of Basal Eurasian has been chewed over. See for example: http://www.anthrogenica.com/showthread.php?3481-Basal-Eurasian-and-ASI-Split&p=59232&viewfull=1#post59232.

Neo
01-18-2015, 12:11 PM
DNA Tribes does not provide professional scientific reviews. It produces laughably incompetent newsletters for its unfortunate clients, who have already been ripped off by actually paying good money for a test that cannot tell them anything like the claims made for it. See http://www.anthrogenica.com/showthread.php?3212-Why-I-do-not-recommend-DNA-tribes I wouldn't bother to read their attempts to guess the meaning of the paper by Lazaridis et al. David is actually citing the latter paper and has it right.

This is in any case a digression from the topic of this thread.

What ever the case may be, Basal Eurasian is not generally not detected in Europeans. ENF is detected in Europeans at variable amounts.But ENF itself ~80% Basal Eurasian. The other non-Basal Eurasian components of ENF,may be non-Levantine-tainted Caucasus admixture.

Southern Italians,Sardinians, Basques,and Cypriots stream towards ''ENF'' for 2 reasons.


1) There is recent admixture of Arabian and Levantine admixture(which has Basal Eurasian) in these aforementioned Euro-Mediterranean groups.

2) There is also prehistoric Neolithic Caucasian admixture in Basques,Cypriots,Sardinians, and a few other European populations of the Mediterranean.

Levantine Eurasians have minute amounts of Basal Eurasian.

Jean M
01-18-2015, 12:25 PM
What ever the case may be, Basal Eurasian is not generally not detected in Europeans.

It would be helpful if you would post anything about Basal Eurasian in threads which discuss it. It would be helpful if you posted about Europeans in threads which discuss Europeans, rather than hijacking a thread on another topic, almost forcing others to respond to you here, taking over a thread which is intended for the discussion of migrations to South Asia. I am not going to prolong this digression by responding further here.

Perhaps a moderator might consider moving the irrelevant posts.

Neo
01-18-2015, 12:37 PM
It would be helpful if you would post anything about Basal Eurasian in threads which discuss it. It would be helpful if you posted about Europeans in threads which discuss Europeans, rather than hijacking a thread on another topic, almost forcing others to respond to you here, taking over a thread which is intended for the discussion of migrations to South Asia. I am not going to prolong this digression by responding further here.

Perhaps a moderator might consider moving the irrelevant posts.

Perhaps the mod can merge some of the posts in this discussion of Basal Eurasian into this thread (http://www.anthrogenica.com/showthread.php?3433-Waves-of-migration-into-South-Asia/page7)you just mentioned instead of deleting it. Although it is a bit off topic it is not irrelevant in ancient genomic studies.I do regret for this thread straying away from the subject at hand.

jeanL
01-18-2015, 10:04 PM
What ever the case may be, Basal Eurasian is not generally not detected in Europeans. ENF is detected in Europeans at variable amounts.But ENF itself ~80% Basal Eurasian. The other non-Basal Eurasian components of ENF,may be non-Levantine-tainted Caucasus admixture.

Southern Italians,Sardinians, Basques,and Cypriots stream towards ''ENF'' for 2 reasons.


1) There is recent admixture of Arabian and Levantine admixture(which has Basal Eurasian) in these aforementioned Euro-Mediterranean groups.

2) There is also prehistoric Neolithic Caucasian admixture in Basques,Cypriots,Sardinians, and a few other European populations of the Mediterranean.

Levantine Eurasians have minute amounts of Basal Eurasian.

Not sure where you are getting your info from, but Basques(Who are not Euro-Mediterraneans to begin with, Mediterranean comes from bordering the Mediterranean sea) do not have any recent Middle Eastern admixture, moreover they do not have excess Middle Eastern admixture compared to other Southern Europeans, in fact they stand out by having lower Middle Eastern admixture, and higher WHG admixture compared to Spaniards, Italians, and people from the Balkans, in the latest K8 calculator Basques have about 44-45% WHG in the higher Near Eastern estimate. So please, if you gonna make wild claims back them up with some sort of data, otherwise you should read the guidelines of the forum before posting.

i.e.

https://docs.google.com/spreadsheets/d/1684wMM_ZJFoxcxJXK0jkVgeGGEVl5Nw3-Moc_IFrlOs/edit?pli=1#gid=1051326962 (ANE_K7)

French_Basque(n=21) ENF_average=23.29%, WHG-UHG_average=66.72%
Spanish_Pais_Vasco(n=8) ENF_average=24.06%, WHG-UHG_average=65.11%

Compare to Western Europeans:

French(n=28) ENF_average=23.25%, WHG-UHG_average=61.04%

Compare to Southern Europeans

South_Italian(n=18) ENF_average=58.35%, WHG-UHG_average=30.86%

Cyprian(n=11) ENF_average=71.71%, WHG-UHG_average=18.64%(Not trying to be mean right now, but you really lost me when you group Basques with Cypriots)

I really don't have time right now to compute all the other averages, but anyone with a pair of eyes can see that compare to other Iberians Basque do score both higher in WHG department, and lower in the ENF, or Near Eastern department. Now compare to Southern Italians, Greeks, Bulgarians, Cypriots(The Cypriots are not even comparable to other Europeans, let alone Basques), they score much much higher WHG and much much lower ENF/Near Eastern.

Here is West_Eurasian K8

https://docs.google.com/spreadsheets/d/1kd9Q9vFrL1Cra9ayqMYVFKXrUdnThmQJVMtjczLhoTs/edit?pli=1#gid=74932529 (West_EurasianK8)

According to a user by the name of "Jesus" another user by the name "Alamut" was kind enough to compile these maps with the population averages for the different component in the newest test.

Near-Eastern
http://i60.tinypic.com/2zfqxpt.jpg

WHG

http://i61.tinypic.com/4zvlh3.jpg

ANE


http://i57.tinypic.com/23w2vr8.jpg

Neo
01-18-2015, 11:11 PM
Not sure where you are getting your info from, but Basques(Who are not Euro-Mediterraneans to begin with, Mediterranean comes from bordering the Mediterranean sea)



i.e.

All Spaniards and Portgugues (including Basques ) are referred to as Mediterrenean and considered Mediterrnean like Italy and Greece.




Basques do not have any recent Middle Eastern admixture, moreover they do not have excess Middle Eastern admixture compared to other Southern Europeans, in fact they stand out by having lower Middle Eastern admixture, and higher WHG admixture compared to Spaniards, Italians, and people from the Balkans, in the latest K8 calculator Basques have about 44-45% WHG in the higher Near Eastern estimate. So please, if you gonna make wild claims back them up with some sort of data, otherwise you should read the guidelines of the forum before posting.


I would actually agree with this , but there is no need to act erractic about it , my point was to state that Sardinians,Sicilians,and Cypriots are groups that have traces of Caucasian admixture.Just because I made an error and grouped the Basques in with these ethnic groups that retain Levantine admixture, does not mean I am completely wrong.These aformentioned groups are said to be long surving ethnicities (dating back to the Mesolithic)in Southern Europe that are in the vicinity of the Mediterranean and have a large bulk of their ancestors that may of traveled to Europe from the Anatolia via Cyprus. <-Link_> (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4046922/)

If you look at my previous post about Basques ,I have said they are a group of people who don't have that much non-local admixture. The condescending tone is not needed.

Humanist
01-19-2015, 12:41 AM
According to a user by the name of "Jesus" another user by the name "Alamut" was kind enough to compile these maps with the population averages for the different component in the newest test.

If that spot in N Syria/Turkey is supposed to denote the position of ZephyrousMandaru, the maps are not very accurate.

Neo
01-19-2015, 03:14 AM
It is not necessarily basal to everybody, especially if it represents a later arrival from Africa
For all I know, the later migrants had different genetics. Also, basal Eurasian does have affinity to subsaharan African and it is a higher affinity than all other ancestral Eurasian types.I am thinkinig a much later arrival for basal Eurasian.

Both of these assertions are in agreement with what I have said in the ‘’Waves Of Migration In South Asia’’ (http://www.anthrogenica.com/showthread.php?3433-Waves-of-migration-into-South-Asia/page8&p=65021#post65021) thread.




Link
(http://www.anthrogenica.com/showthread.php?3433-Waves-of-migration-into-South-Asia&p=65008&viewfull=1#post65008)
Post any peer reviewed where it discusses the amounts of Basal Eurasian in Europeans, I haven't seen it..

Only Eurasian groups that have a strongest affinity to Basal Eurasian Arabians/Bedouins. Levantines themselves have a bit of Bedouin admixture ,as a result on PCA plots they stream to ENF(which is ~70-80% Basal Eurasian).






There seems to be a confusion here between modern and ancient DNA. In the Lazaridis paper 'Basal Eurasian' was a label for a 'ghost' ancient population of which we do not yet have an ancient representative. It was deduced from its presence in EEF to have been in the Near East in the Neolithic. It does not make any difference if some of this population entered Africa after splitting from the original Out-of-Africa migration.

There also seems to be a confusion over the term 'basal' which Megalophias has clarified. A lot of people have assumed that it means 'the population from which all Eurasians descend', when in fact it represents an early split in that population, with one group (the basal) going off into such isolation from the rest that it does not contribute to all subsequent Eurasians, only some of them.

'Ancestral Eurasian' would be a good term for the ancestral group from which all Eurasians descend, but it is now looking like we have two waves out of Africa, which rather confuses the matter.

EEF was the original admixture before ANE was extracted from it, the result begot ‘’ENF’’. The reason why Davidski denotes ENF is Near Eastern, is because it streams towards Caucasus populations and to a lesser degree Levantine populations.


It does not. Lazaridis makes it absolutely clear that 'Basal Eurasian' is not a subsequent arrival from Sub-Saharan Africa. It split away from the group that had left Africa. If you think of it as the autosomal equivalent to Y-DNA E, it might help to visualise it. Africa today is full of E. It spread with farmers to almost obliterate the more ancient Y-DNA haplogroups of Africa, A and B, associated with hunter-gatherers.

Basal does not mean ancestral, as Megalophias explained. 'Basal Eurasian" does not equal "Ancestral Eurasian." In other words "Basal Eurasian" does not mean the OOA ancestral group. "Basal Eurasian" is a group that split away from the OOA ancestral group. The OOA ancestral group = Ancestral Eurasian = the ancestors of all people native to the world outside Africa.

What complicates matters is that lots of people living in Africa today also have DNA that descends from the OOA group.



The problem with this is, many Eurasians are devoid of Basal Eurasian admixture. Claiming Basal Eurasian derived from an ancient ghost population that roamed Eurasia, would be inaccurate and hard to substantiate. Being that there isn't any admixture (of even minute traces of Basal Eurasian) in places like the Gedrosia, Iranian regions,Europeans, and other East Eurasian populations.





I think you are right and it is the most plausible scenario . Stuttgart probably had some recent African ancestry.
Assuming this is the case, I would agree with basal Eurasian being an early split from ooa. The actual basal Eurasian won't have any recent African. The lazaridis basal numbers would be a mix.

This is another hypothesis I made in this thread (http://www.anthrogenica.com/showthread.php?3433-Waves-of-migration-into-South-Asia&p=65017&viewfull=1#post65017) , glad to see I am not the only one who has this notion. Basal Eurasian can even date older than current African population clusters like Omotic, ACs, Nilotic ACs,Cushitic ACs ,etc but it could of very well have originated on the African continent. Basal Eurasian’’ might of emerged at a later period of the OOA migrations but likely predates the Horner/Cushitic Cluster,Niger-Congo Cluster,Nilotic cluster ,Omotic cluster and Pygmy clusters. Basal Eurasian is not a parental admixture to most Eurasian populations and most OOA wouldn’t of carried this admixture. Pygmies and Mbuti are devoid of these components. Its possible,that Basal Eurasian is older than modern African components like Nilotic,Horner,West African,etc in contrast it would be younger to archaic African admixtures like those found in Pygmies and San. Rendering Basal Eurasian intermediate in age between San/Pygmy in contrast to Nilotic,Omotic,Bantu African,Cushitic, and Other Current African admixtures.Thats my take.




I think you mean ancestral, but in either case, only if we are talking about ancient Africans before the departure of the OOA group(s). Africa did not float off to some inaccessible place after the OOA groups left. ;) As far as I can see, people kept coming and going between Africa and Asia from the Palaeolithic onwards. So there is Eurasian DNA in modern Africans. There is even some in the modern Koisan, whom geneticists have often used as a proxy for the ancestors of the OOA group. http://www.pnas.org/content/111/7/2632




Only faulty genetic studies would claim Khoisans have non-local/Eurasian admixture .There are other studies that say the contrary. Khoisians are probably thee most indigenous group to Africa. If Khoisians have Eurasian admixture how come the other neighboring African populations don’t have this Eurasian admixture? D.Shriner et al 2014 (http://www.nature.com/srep/2014/140813/srep06055/extref/srep06055-s1.pdf), has San people at 95% CS admixture and 5% Pygmy.

Its like saying Saami have Turkic or Caucasian admixture when they are probably one of purest of Northern Europeans.Its like saying the Basque are mixed with non-European components when they are the most isolated group in Europe. Khosian culture dates to 50,000 years ago to Late Stone Age. They are the oldest human ethnicity in Africa (let alone the planet) and have a high internal genetic diversity.Only some Khosian groups have minor traces of West African ancestry ( and its probably due to Bantu interaction).







Study Suggests African Khoisan Hunter-Gatherers Remained Isolated, Represented Largest Population (https://www.genomeweb.com/sequencing-technology/study-suggests-african-khoisan-hunter-gatherers-remained-isolated-represented)



Two of the Khoisan genomes, from the Ju/'hoansi group, appear to show no genetic contributions from other human populations, suggesting that members of the group may have remained genetically isolated for up to 150,000 years...

Their analysis, which employed four different methods, showed that the Ju/'hoansi couple had no evidence of admixture from non-Khoisan groups, whereas the other Khoisan genomes displayed a small percentage of western African ancestry, and Archbishop Tutu showed both western African and southern Khoisan ancestries.

The finding was possible, he said, because of the care taken by the researchers to obtain samples from very isolated Khoisan tribes that have had not only geographic but also cultural barriers to mixing with other populations.

Based on that analysis, they concluded that the Khoisan split from other African populations around 100,000 to 150,000 years ago and maintained high genetic diversity throughout, and the largest population. Non-Khoisans, on the other hand, saw a decline in their effective population size and lost more than half of their diversity over the last 30,000 to 120,000 years.
About 40,000 to 60,000 years ago, humans then started to migrate out of Africa, which led to the split between African and non-African populations and a steep decline in genetic diversity in the latter.








I already have done. Africa is full of people partly descended from farmers from the Near East. Farmers can out-breed foragers. This is what happened in Europe. This is what happened in Africa. A lot of the descendants of early farmers in Africa are carrying Y-DNA E. Some descendants of EEF farmers are carrying Y-DNA E.


Wherever Y-DNA E was actually born does not matter. It descends from DE which is a branch under CT, which seems to be the key group of OOA. So E is descended from the OOA group.

Picture a scene in which a few people descended from the OOA group mill around in Saudi Arabia and then wander back into East Africa, who have descendants millennia later who move into the Levant as the Holocene greens the Sahara. They take to farming as it moves south into the Levant. Then comes a climate crisis and so their descendants look for other places to farm. Mainly they go south into North Africa, as that is nearest. From there it filters slowly south.

I think if you yourself can propose a native population becoming out bred by a non-native population, you can also see it possible that non-African getting out bred in Africa, especially when there is much more abundance of Africans (which means autochthonous African admixture) on the continent(in any sub-region). As an example, R1B-V88 carriers in the T-Chad region of West Africa ,which exhibit no traces of Eurasian DNA what so ever. It only takes 9 generations (at the 9th generation it becomes a negligible, <~0.5% the AC)for an admixture from an ancestor/great grandparent to be deleted.



Well, unless Wikipedia is wrong, CT originated in Africa and there is a possibility that DE originated in Africa. If A and B are the only indigenous African haplogroups, what happened to the original CT or descendants? It all died out leaving no descendants behind? Now, D is obviously Asian, but there is a possibility that DE originated in Africa, and left behind E in the original CT homeland, meaning East Africa.
CT has two branches: CF and DE. If CF is Asian and DE is also Asian, then only A and B are native African? I find that very hard to believe.
What I am saying is, sure, CT is the ooa group, but there is a chance that E stayed in Africa for a while and a later second wave of E carriers spread that haplogroup around.
Supposedly E arose 50k years ago. CT almost 70k years ago per Wikipedia. That's a difference of 20k years, which is enough time to change one's genetic profile.
Come to think of it, even Chechens had their shared drift numbers reduced. Which means this is not just a Southern European thing.

I’m agree with you on this too. If ''D'' migrated back to Africa, we would simply see more traces of D in Gedrosia ,Iran and the Arabian peninsula, just my personal opinion. CT is found in Fertile Crescent and so is DE, but if there was a back migration of DE ,it would be observed in the Middle East , Arabian peninsula or the Gulf of Persia region. I am of the school of thought that CT and DE was out bred and went extinct in Africa,by other competiting African paleolothic culture that carried the haplogroup E (and its descendants). We can also see A and B get reduced to lower numbers of competing groups. This is a better theory than CT and DE went extinct in the Middle East ,Iran, Gedrosia or South Asia. Simple Fortunately though E* has been found in Africa.More importantly, DE* has been found in Africa as well,of the 5 DE*that have been discovered in Africa, three are paraphyletic.



http://www.genetics.org/content/165/1/229.full


The new haplogroup, labeled DE* according to the nomenclature of the Y CHROMOSOME CONSORTIUM (2002), has been found in 5 Nigerians (from different villages, languages, ethnic backgrounds, and paternal birthplaces) from a data set of >8000 men worldwide, including 1247 Nigerians







Kostenki 14 already is Europeanlike 36k years ago, and has all the components that modern Europeans do. Yet, MA-1 (who lived 14k years after) is not admixed with Stuttgart and WHG. Similarly, Loschbour is a pure WHG sample according to the authors. Something doesn't fit here, namely K14 being very Europeanlike 36K years ago. Honestly, the mistake here that the authors are making is trying to deduce ancestry based on 3-4 samples.
I feel that we are in the early stages of using ancient DNA samples to study population genetics. 10 years from now, the picture is going to be very different.

My point exactly, all of the extractions aDNA explains a lot, but it doesn’t mean these aDNA are totally sufficient with depicting what ancient populations autosomal components were completely composed of .There is still potential missing aDNA and paleolithic samples to extract ancient genomes from(ie Levantine Paleolithic samples).Many larger intra-populations dating back in time derive from smaller populations (this is realistic since we know human populations in prehistoric times were smaller). If a small ancient population has two splinter groups that diverge from each other say ~20,000 years ago they have the inertia to make a present day cluster. As an example we see the ancient West Eurasian admixture become basal to other components like WHG and ENF.

Jean M
01-19-2015, 11:32 AM
EEF was the original admixture before ANE was extracted from it, the result begot ‘’ENF’’.

Some confusion here. In the original Lazaridis 2014 paper, EEF = Early European Farmer. This is an actual genome cluster from the remains of several early European farmers. It does not contain ANE.

People online may well be tossing around acronyms like ENF, which I assume to be Early Neolithic Farmer, but we don't have a genome from the early Neolithic Near East. The best guess would be EEF minus WHG. Is that what you mean?

Jean M
01-19-2015, 11:59 AM
The problem with this is, many Eurasians are devoid of Basal Eurasian admixture. Claiming Basal Eurasian derived from an ancient ghost population that roamed Eurasia, would be inaccurate and hard to substantiate.

Lazaridis et al 2014 are not claiming Basal Eurasian to derive from an ancient population that roamed the whole of Eurasia. Quite the contrary. It appears to be a breakaway group from the OOA community which emphatically did not roam the whole of Eurasia, otherwise we would expect it to have been present both in Mesolithic Europeans and in Mal'ta boy. Lazaridis et al sensibly deduced that it was a ghost population that had kept much to itself until blending with other occupants of the Near East in the Neolithic. That is why it looks a good fit for Y-DNA E, though I make that point simply because it is easier for people to visualise. We know that Y-DNA E is not all over Eurasia.

The discovery of Basal Eurasian in the Palaeolithic Kostenki 14 rather threw a spanner in the works, but his was presumably a lineage that did not survive the LGM in Europe.

J Man
01-19-2015, 12:25 PM
ANE was never extracted from EEF because EEF never contained any ANE. There is however WHG alleles in the EEF component as it is a hybrid component of Near Eastern and WHG alleles but Davidski has sorted all of this out now in his new K8 test.

Jean M
01-19-2015, 01:18 PM
ANE was never extracted from EEF because EEF never contained any ANE. There is however WHG alleles in the EEF component as it is a hybrid component of Near Eastern and WHG alleles but Davidski has sorted all of this out now in his new K8 test.

Perhaps you could summarize the results for those of us who don't follow David's work in detail. Has he managed to identify Basal Eurasian? Where is it found in modern populations?

J Man
01-19-2015, 01:52 PM
Perhaps you could summarize the results for those of us who don't follow David's work in detail. Has he managed to identify Basal Eurasian? Where is it found in modern populations?

David did not manage to isolate Basal Eurasian completely but he did manage to find a component that is mainly made up of Basal Eurasian alleles. The other part (minority) is made up of alleles that are either distantly related to or ancestral to the WHG component. It is called Near_Eastern in his new K8 test and it is found in it's highest frequencies in Samaritans, Saudis and Bedouins.

Neo
01-19-2015, 01:53 PM
Lazaridis et al 2014 are not claiming Basal Eurasian to derive from an ancient population that roamed the whole of Eurasia. Quite the contrary. It appears to be a breakaway group from the OOA community which emphatically did not roam the whole of Eurasia, otherwise we would expect it to have been present both in Mesolithic Europeans and in Mal'ta boy. Lazaridis et al sensibly deduced that it was a ghost population that had kept much to itself until blending with other occupants of the Near East in the Neolithic. That is why it looks a good fit for Y-DNA E, though I make that point simply because it is easier for people to visualise. We know that Y-DNA E is not all over Eurasia.

The discovery of Basal Eurasian in the Palaeolithic Kostenki 14 rather threw a spanner in the works, but his was presumably a lineage that did not survive the LGM in Europe.

This is what I was alluding to in my post. The Paleolithic Humans in Africa that carried the Basal Eurasian component were counterparts to the OOA migration. The carriers of Basal Eurasian either remained stationary in their region of Horn of Africa(maybe Arabia), or drifted off in another direction of the OOA migrants. The primary OOA migrants and secondary OOA migrants most likely did not carry Basal Eurasian components. It's possible many splintered populations from Horn of Africa (carrying the Basal Eurasian component) roamed Eurasia, but ended up being dead end population groups in most places. But in some minority areas ,splintered groups carrying Basal Eurasian subsequently caused their offspring to produce hybrids or their component(BA) became absorbed by the local populations(which caused Basal Eurasian to eventually become dissipated in the area).Places like Stuttgart are an example of this scenario.

Jean M
01-19-2015, 02:05 PM
This is what I was alluding to in my post. The Paleolithic Humans in Africa that carried the Basal Eurasian component were counterparts to the OOA migration.

No. Basal Eurasian is an offshoot of the OOA migration group. It descends from the OOA group. It does not represent a fresh migration from Africa. I quote Lazaridis et al 2014:


However, the basal Eurasian population shares much of the genetic drift common to non-African populations after their separation from Africans, and thus does not appear to represent gene flow between sub-Saharan Africans and the ancestors of non-Africans after the out-of-Africa bottleneck (Supplementary Information section 14).

Here is the tree from Lazaridis.

3449

It seems perfectly possible that the carriers of Basal Eurasian did not on the whole stray far from Arabia and adjacent regions in the Palaeolithic, while the rest of the OOA group scattered much more widely.

Here is the original paper: The final version in Nature (behind paywall): http://www.nature.com/nature/journal/v513/n7518/full/nature13673.html

Earlier draft in full: http://biorxiv.org/content/biorxiv/early/2013/12/23/001552.full.pdf

Neo
01-19-2015, 02:17 PM
No. Basal Eurasian is an offshoot of the OOA migration group. It descends from the OOA group. It does not represent a fresh migration from Africa. Here is the tree from Lazaridis.

3449

It seems perfectly possible that the carriers of Basal Eurasian did not on the whole stray far from Arabia and adjacent regions in the Palaeolithic, while the rest of the OOA group scattered much more widely.

Which Eurasian group is an offshoot of the OOA migration?One would think which area of Eurasia, would Basal Eurasian remain stationary and dormant?

Jean M
01-19-2015, 02:45 PM
Which Eurasian group is an offshoot of the OOA migration?

See the tree which I posted from Lazaridis et al 2014. Basal Eurasian is their name for a 'ghost' population i.e. one for which they do not have an ancient sample, but for which they deduce an existence, since a genetic component appears in EEF which they did not find in WHG or ANE. Said component represents some 44% plus or minus 10% of EEF.

They logically deduce that BE arrived in Europe in the Neolithic. They further logically deduce that BE represents a population not present in Palaeolithic Europe and therefore not present in the Palaeolithic population of the Levant, from which most of the Palaeolithic population of Europe can be deduced to derive on archaeological grounds. The exception is the group that we now know entered Europe via the Caucasus, which had a slightly later origin. It is this group which is represented by Kostenki 14, with mtDNA U2 and some BE.

3451

3452

I show the dotted line to Kostenki originating not far from the Levant, but that is just guesswork. That trail could have by-passed the Levant.

Jean M
01-19-2015, 03:01 PM
One would think which area of Eurasia, would Basal Eurasian remain stationary and dormant?

I doubt very much that it was stationary. Eurasia is a very big place. The Palaeolithic population of it was tiny. Really, really tiny. The Palaeolithic population of Europe has been estimated at 4400–5900 inhabitants. These were small hunting bands, widely scattered. It would be no problem whatsoever for a group splitting off from OOA to become sufficiently isolated for genetic drift to occur within that group over time (so making it distinguishable from other branches from OOA). That is exactly what happened in other cases for which we do have more data, so why should it not have happened to the proposed offshoot BE? A proposed homeland in Arabia, moving back to Africa to avoid the desertification in the LGM, and then into the Near East in the Neolithic is perfectly plausible and indeed fits other kinds of evidence.

Jean M
01-19-2015, 03:32 PM
David did not manage to isolate Basal Eurasian completely but he did manage to find a component that is mainly made up of Basal Eurasian alleles. The other part (minority) is made up of alleles that are either distantly related to or ancestral to the WHG component. It is called Near_Eastern in his new K8 test and it is found in it's highest frequencies in Samaritans, Saudis and Bedouins.

That's very helpful J Man. I think I now have it. It is this spreadsheet yes? https://docs.google.com/spreadsheets/d/1x8pm8sVcHqceiNFJMO082kxaBF5ePr4__bAK05VQRFw/edit#gid=62882571

Am I understanding these figures correctly?
The Basque French are nearly 50% Near Eastern and the rest mainly WHG?
The Armenians are around 75% - 80% Near Eastern?
The Orcadians are around 36% to 39% Near Eastern?

Hando
01-19-2015, 04:08 PM
They logically deduce that BE arrived in Europe in the Neolithic. They further logically deduce that BE represents a population not present in Palaeolithic Europe and therefore not present in the Palaeolithic population of the Levant, from which most of the Palaeolithic population of Europe can be deduced to derive on archaeological grounds. The exception is the group that we now know entered Europe via the Caucasus, which had a slightly later origin. It is this group which is represented by Kostenki 14, with mtDNA U2 and some BE.

3451

3452

I show the dotted line to Kostenki originating not far from the Levant, but that is just guesswork. That trail could have by-passed the Levant.
You say that the group represented by Kostenki 12 had a slightly later origin. Compared to who? And when?

Why is the dotted blue Uluzzian going to Kostenki via Caucasus as well as to Italy via Anatolia and the Balkans? Were there in fact two trails of the same group?

Hando
01-19-2015, 04:16 PM
David did not manage to isolate Basal Eurasian completely but he did manage to find a component that is mainly made up of Basal Eurasian alleles. The other part (minority) is made up of alleles that are either distantly related to or ancestral to the WHG component. It is called Near_Eastern in his new K8 test and it is found in it's highest frequencies in Samaritans, Saudis and Bedouins.

If Samaritans, Saudis and Bedouins are mainly Basal Eurasian, then does it not follow that the Near Easter component in EEF were most similar to modern day Saudis/Bedouins? I was under the impression that the Near Eastern component in EEF was not similar to Saudis and that it is only during the historical period that the Saudi like genes migrated into the old EEF homeland of the Levant?
And if 44% of EEF was Basal how much of the rest was also Near Eastern as opposed to WHG?

Sangarius
01-19-2015, 04:48 PM
If Samaritans, Saudis and Bedouins are mainly Basal Eurasian, then does it not follow that the Near Easter component in EEF were most similar to modern day Saudis/Bedouins? I was under the impression that the Near Eastern component in EEF was not similar to Saudis and that it is only during the historical period that the Saudi like genes migrated into the old EEF homeland of the Levant?
And if 44% of EEF was Basal how much of the rest was also Near Eastern as opposed to WHG?

When the African admixture in Saudis and Bedouins is accounted for, they show the highest similarity to the Near Eastern admixture carried by EEF.
Davidski has modelled Stuttgart as 72% Near Eastern and 28% WHG. The Near Eastern AC is afaik 70% Basal Eurasian. That makes Stuttgart 50% Basal Eurasian and 22% Near Eastern UHG.

parasar
01-19-2015, 04:50 PM
Some confusion here. In the original Lazaridis 2014 paper, EEF = Early European Farmer. This is an actual genome cluster from the remains of several early European farmers. It does not contain ANE.

People online may well be tossing around acronyms like ENF, which I assume to be Early Neolithic Farmer, but we don't have a genome from the early Neolithic Near East. The best guess would be EEF minus WHG. Is that what you mean?

ENF should not be isolated without confirmation from an ancient genome. EEF minus West Eurasian (hunter gatherer ancestral to WHG)= Basal



...
Here is the original paper: The final version in Nature (behind paywall): http://www.nature.com/nature/journal/v513/n7518/full/nature13673.html

http://genetics.med.harvard.edu/reich/Reich_Lab/Welcome_files/2014_Nature_Lazaridis_EuropeThreeAncestries.pdf

Jean M
01-19-2015, 05:21 PM
ENF should not be isolated without confirmation from an ancient genome.

I couldn't agree more.


EEF minus West Eurasian (hunter gatherer ancestral to WHG)= Basal

Basal Eurasian is only one component of the Near Eastern part of EEF. Here is the proposed model for Stuttgart from Lazaridis et al 2014:

3455

We would expect the Near Eastern component to contain an element related to WHG, since the Mesolithic Europeans were descended from Palaeolithic incomers from/via the Near East. What complicates matters is that Stuttgart was not fresh off the boat from the Near East and so represents a mixture with WHG as well.

Jean M
01-19-2015, 05:29 PM
You say that the group represented by Kostenki 12 had a slightly later origin. Compared to who? And when?

The numbers on the map represent the earliest radiocarbon dates for human tools of these cultures in thousands of years ago. Kostenki 14 is the dot labelled 40 = 40,000 years ago.


Why is the dotted blue Uluzzian going to Kostenki via Caucasus as well as to Italy via Anatolia and the Balkans? Were there in fact two trails of the same group?

The dashed blue line is not Uluzzian. It is Proto-Aurignacian and there is indeed similar material along these routes. That map was prepared for Ancestral Journeys, of which I know you have a copy. You will find it on page 51, with the accompanying text, with references.

parasar
01-19-2015, 05:36 PM
I couldn't agree more.



Basal Eurasian is only one component of the Near Eastern part of EEF. Here is the proposed model for Stuttgart from Lazaridis et al 2014:

3455

Without an ancient near eastern genome we don't have a Near Eastern part of EEF.
Basal is a ghost population inferred from the Neolithic genome and (its absence in) ANE and WHG genomes.
"EEF minus West Eurasian (hunter gatherer ancestral to WHG)= Basal" can be seen in the tree you posted at #66 above.

Jean M
01-19-2015, 06:57 PM
Without an ancient near eastern genome we don't have a Near Eastern part of EEF.

I agree. We should simply wait for aDNA from the Near Eastern Neolithic. I have made no secret of my exasperation that Lazaridis et al 2014 were so enthusiastic about their supposed BE that they just had to include it in their paper, before actually being able to identify it properly from aDNA. The result has been an explosion of speculation leading nowhere. It just seems to get wilder and wilder.


"EEF minus West Eurasian (hunter gatherer ancestral to WHG)= Basal" can be seen in the tree you posted at #66 above.

Yes I know. What I'm saying is that the Western Eurasian in EEF is not modelled as simple, straightforward 100% WHG. In other words it is not modelled as 100% the result of mixing with hunter-gatherers in Europe. The deduction is that early farmers from the Near East arrived in Europe with a Western Eurasian component already in their gene pool.

Neo
01-19-2015, 07:25 PM
See the tree which I posted from Lazaridis et al 2014. Basal Eurasian is their name for a 'ghost' population i.e. one for which they do not have an ancient sample, but for which they deduce an existence, since a genetic component appears in EEF which they did not find in WHG or ANE. Said component represents some 44% plus or minus 10% of EEF.

They logically deduce that BE arrived in Europe in the Neolithic. They further logically deduce that BE represents a population not present in Palaeolithic Europe and therefore not present in the Palaeolithic population of the Levant, from which most of the Palaeolithic population of Europe can be deduced to derive on archaeological grounds. The exception is the group that we now know entered Europe via the Caucasus, which had a slightly later origin. It is this group which is represented by Kostenki 14, with mtDNA U2 and some BE.

3451

3452

I show the dotted line to Kostenki originating not far from the Levant, but that is just guesswork. That trail could have by-passed the Levant.




David did not manage to isolate Basal Eurasian completely but he did manage to find a component that is mainly made up of Basal Eurasian alleles. The other part (minority) is made up of alleles that are either distantly related to or ancestral to the WHG component. It is called Near_Eastern in his new K8 test and it is found in it's highest frequencies in Samaritans, Saudis and Bedouins.

How much Basal Eurasian does Kostenki 14? I was reading that it's Y chromosome is of the haplogroup C, just like that of La Brana.Its more related to East Eurasian Y ---DNA and very distantly related to the C haplogroup in modern day Amerindians.I think this represents how widespread the C haplogroup may have once been in Eurasia.

Hopefully finds new discovered Basal Eurasian alleles in Kotenki14 to extract from. Oetzi and Gok2 have Basal Eurasian.Very interesting because Gok2 in Sweden is 5,000 BPand Oetzi in Italy is 5300 BP.I wonder if Kostenki14 belonged to people who are the ancestors Oetzi and Gok2? Its possible for Gok2 since they are in vicinity of Northern Eurasia .

Jean M
01-19-2015, 08:03 PM
How much Basal Eurasian does Kostenki 14?

Who knows? Here is the relevant extract from Andaine Seguin-Orlando et al., Genomic structure in Europeans dating back at least 36,200 years, Science Express, 6 November 2014:


In addition, a sizeable component of K14’s ancestry observed in the model-based clustering analyses is predominant in contemporary Middle Eastern/Caucasus (ME/C) populations and Neolithic ancient genomes (NEOL) (Gok2, Iceman, Stuttgart), but absent in MA1 or MHGs (Fig. 1B and fig. S20). This component has been associated with a suggested “basal Eurasian” lineage contributing to NEOL, to explain an observed increase in allele sharing between MHGs / MA1 and East Asians compared to NEOL (21). Since K14 shows the same pattern as NEOL, a parsimonious explanation would be that K14 also derives some ancestry from a related “basal Eurasian” lineage.


I wonder if Kotenki14 belonged to people who are the ancestors...

It is much more likely that he left no descendants beyond the Last Glacial Maximum. The human population of Europe contracted at that time almost to the point of dying out. Many lineages will have been lost. If he belonged to a lineage that survived to the Mesolithic, we would expect European Mesolithic hunter-gatherers to have BE and so far no Mesolithic sample has it.

Leeroy Jenkins
01-19-2015, 08:06 PM
It is much more likely that he left no descendants beyond the Last Glacial Maximum. The human population of Europe contracted at that time almost to the point of dying out. Many lineages will have been lost. If he belonged to a lineage that survived to the Mesolithic, we would expect European Mesolithic hunter-gatherers to have BE and so far no Mesolithic sample has it.

The authors of the paper seem to think Kostenki represents a dead end, as they did not draw a contribution line from him to modern Europeans in their model.

http://1.bp.blogspot.com/-jlF6eSOWmnk/VFwpvCk9MjI/AAAAAAAAJ1o/lkmfDp204OU/s1600/F2.large.jpg

Neo
01-19-2015, 09:34 PM
Who knows? Here is the relevant extract from Andaine Seguin-Orlando et al., Genomic structure in Europeans dating back at least 36,200 years, Science Express, 6 November 2014:





It is much more likely that he left no descendants beyond the Last Glacial Maximum. The human population of Europe contracted at that time almost to the point of dying out. Many lineages will have been lost. If he belonged to a lineage that survived to the Mesolithic, we would expect European Mesolithic hunter-gatherers to have BE and so far no Mesolithic sample has it.




There are some populations in the Middle East that became obsolete as well(Qafzeh and Skuhl) are examples of this.Some of them date back to 90-70 kya.



http://www.hindawi.com/journals/ijeb/2011/615094/

Although the earliest dated modern humans outside of Africa were identified in the Middle East ~90 kya (5, 8–11), there was no continuous occupation of regions outside of Africa until ~60–40 kya

But the point is whether Kostenki 14,Oetzi and Gok2 retain little or more Basal Eurasian admixture than Stuttgart,hopefully new Basal Eurasian alleles can be from extracted these samples (or maybe its already been done).



Without an ancient near eastern genome we don't have a Near Eastern part of EEF.
Basal is a ghost population inferred from the Neolithic genome and (its absence in) ANE and WHG genomes.
"EEF minus West Eurasian (hunter gatherer ancestral to WHG)= Basal" can be seen in the tree you posted at #66 above.


https://docs.google.com/spreadsheets/d/1x8pm8sVcHqceiNFJMO082kxaBF5ePr4__bAK05VQRFw/edit#gid=62882571

The ENF/Near Eastern Ks need to be refined,like the Near Eastern admixture in this K8 run a little too high. Italians and Greeks score >60% Near Eastern which is a bit abormal.

J Man
01-19-2015, 09:41 PM
That's very helpful J Man. I think I now have it. It is this spreadsheet yes? https://docs.google.com/spreadsheets/d/1x8pm8sVcHqceiNFJMO082kxaBF5ePr4__bAK05VQRFw/edit#gid=62882571

Am I understanding these figures correctly?
The Basque French are nearly 50% Near Eastern and the rest mainly WHG?
The Armenians are around 75% - 80% Near Eastern?
The Orcadians are around 36% to 39% Near Eastern?

Yes correct.

Generalissimo
01-19-2015, 10:41 PM
The ENF/Near Eastern Ks need to be refined,like the Near Eastern admixture in this K8 run a little too high. Italians and Greeks score >60% Near Eastern which is a bit abormal.

The results correlate very well with the PCA positions of Mesolithic, Neolithic, and modern Europeans and Near Eastern populations. So the levels of Near Eastern admixture in Europe in the K8 analysis aren't too high.

There's nothing abnormal about Italians and Greeks being over 60% Near Eastern. There's no evidence anywhere to suggest that they should be less Near Eastern.

jeanL
01-19-2015, 11:23 PM
That's very helpful J Man. I think I now have it. It is this spreadsheet yes? https://docs.google.com/spreadsheets/d/1x8pm8sVcHqceiNFJMO082kxaBF5ePr4__bAK05VQRFw/edit#gid=62882571

Am I understanding these figures correctly?
The Basque French are nearly 50% Near Eastern and the rest mainly WHG?
The Armenians are around 75% - 80% Near Eastern?
The Orcadians are around 36% to 39% Near Eastern?

Here are the averages for the Basques on the higher near eastern run:

French_Basque(n=21) Near_Eastern_average=47.42%(Min:44.22% Max:50.14), WHG_average=45.80%(Min:43.52% Max:48.53%)
Spanish_Pais_Vasco(n=8) Near_Eastern_average=47.37%(Min:46.03% Max:49.70%), WHG_average=44.92%(Min:44.44% Max:46.15%)

Neo
01-20-2015, 04:22 PM
The results correlate very well with the PCA positions of Mesolithic, Neolithic, and modern Europeans and Near Eastern populations. So the levels of Near Eastern admixture in Europe in the K8 analysis aren't too high.

There's nothing abnormal about Italians and Greeks being over 60% Near Eastern. There's no evidence anywhere to suggest that they should be less Near Eastern.


With Greece , I can understand the correlations. When it comes to Italians and French, I would speculate them to have more WHG than ENF. With modern European populations ,we see a Northern European admixture(and Western European admixture) diffusing across Europe.This seems to be the same case with ancient European genomes, it's a bit more WHG(and to a lesser degree ANE from Northeast Europe and Northern Asia) disseminating from the North to South.We see this diffusion with Loschbour,Brana, and Oetzi.

French, Italians(Even Northern Italians) and Sicilians score higher Near East/ENF than Balkan populations(Bosnian,Croatian,Macedonian,Serbian ,etc), its a bit strange and not something one would expect. Italians,Sicilians,and French score over ~50- 60% which is around ~10-20% more than the Balkan populations. I also didn't expect for Finnish,Lithuanian, and Norwegian to have any ENF at all (lol), they score around 20% ENF from my general estimate




Here are the averages for the Basques on the higher near eastern run:

French_Basque(n=21) Near_Eastern_average=47.42%(Min:44.22% Max:50.14), WHG_average=45.80%(Min:43.52% Max:48.53%)
Spanish_Pais_Vasco(n=8) Near_Eastern_average=47.37%(Min:46.03% Max:49.70%), WHG_average=44.92%(Min:44.44% Max:46.15%)


So there is Near Eastern ENF from the Neolithic after all, this is what I suspected about Basques having Neolithic Near East input (in post #68 (http://www.anthrogenica.com/showthread.php?3481-Basal-Eurasian-and-ASI-Split&p=65021&viewfull=1#post65021)). Although I like to think of it Caucasian(less Levantine based).

If ENF is ~70-80% Basal Eurasian, I have to contemplate, what are the rest of the genetic components its made of? Im assuming ~20-30% would be made of residual Near Eastern components found in Neolithic Europe, that may have a affinity for Near Eastern on PCAs maybe?

Hando
01-20-2015, 05:09 PM
The numbers on the map represent the earliest radiocarbon dates for human tools of these cultures in thousands of years ago. Kostenki 14 is the dot labelled 40 = 40,000 years ago.



The dashed blue line is not Uluzzian. It is Proto-Aurignacian and there is indeed similar material along these routes. That map was prepared for Ancestral Journeys, of which I know you have a copy. You will find it on page 51, with the accompanying text, with references.
1)Ok, so Kostenki 14 was 40,000YBP, but you said Kostenki 12 had a slightly later origin. Compared to who?
2)According to the map on page 51 Proto-Aurignacian had two routes. One leading to Kostenki and the other via Anatolia, Balkans, N Italy, S France and N Spain. So just to confirm, were there in fact two trails of the same group?

vettor
01-20-2015, 06:20 PM
When it comes to Italians and French, I would speculate them to have more WHG than ENF. With modern European populations ,we see a Northern European admixture(and Western European admixture) diffusing across Europe.

Pity the french region is not split except for Laz paper

The Laz paper has South-french, North-italians and Bulgarians by the numbers as the "same group".
To conclude , I find your comments irrelevant when you unite Italians as one group or the french in one group, it is not done that way in genetics

Neo
01-20-2015, 06:48 PM
Pity the french region is not split except for Laz paper

The Laz paper has South-french, North-italians and Bulgarians by the numbers as the "same group".
To conclude , I find your comments irrelevant when you unite Italians as one group or the french in one group, it is not done that way in genetics

If we are dealing with population genetics ,it would be logical to compartmentalize the different nationalities by regions .Geographic proximity and land barriers(or lack there of), can affect the population's gene-flow. This would be especially true for Italians, since there is a slight distinction between Northern and South Italians in terms of phenotype. Even Southern Italians would claim Sicilians have a distinctive look from themselves.

I would not take the categories of nationalities and regions within nations for granted.It can make a big difference in averaging. And the authors of the spreadsheet might know it too,as we see can East Sicilians ,South Italian,and North Italian partitioned off.The different regions of Spain are subdivided as well.

Jean M
01-20-2015, 06:53 PM
1)Ok, so Kostenki 14 was 40,000YBP, but you said Kostenki 12 had a slightly later origin. Compared to who?

It is Kostenki 14 that I am talking about. I did not mention Kostenki 12, as far as I know. I know nothing about Kostenki 12.

The Caucasus route leading to Kostenki 14 (40,000 years ago) is later than the main route of entry into Europe over what was then a land bridge SW of what is now the Black Sea. You can see the date 46,000 years ago on the map for that crossing. I am presuming that mtDNA U (older than U2) entered Europe that way. I gave the map for that.


So just to confirm, were there in fact two trails of the same group?

The same group? How could the same group enter Europe 46,000 years ago and also 40,000 years ago? Here is the accompanying text on pp. 51-52:


A third entry into Europe has been termed Proto-Aurignacian, since it shares some features with Aurignacian, such as split-based points. Its tool-set is similar to that of the Levantine Ahmarian, and included bone needles, so useful for making clothing.

Early DNA Evidence
A trail through the Caucasus of material similar to Aurignacian shows people had headed for Europe by a separate route. They can be linked to sites in the Don river valley, Russia, dating from 40,000 years ago, including Kostënki 14 (Illustration 12).


Since there is no better description of this latter culture than 'similar to Aurignacian', I opted to colour that dotted line as Proto-Aurignacian. Maybe I'll have the colour of that line changed in the 2nd edition, since it seems to be causing confusion. (Though what other label I could use, I know not.)

vettor
01-20-2015, 07:19 PM
If we are dealing with population genetics ,it would be logical to compartmentalize the different nationalities by regions .Geographic proximity and land barriers(or lack there of), can affect the population's gene-flow. This would be especially true for Italians, since there is a slight distinction between Northern and South Italians in terms of phenotype. Even Southern Italians would claim Sicilians have a distinctive look from themselves.

I would not take the categories of nationalities and regions within nations for granted.It can make a big difference in averaging. And the authors of the spreadsheet might know it too,as we see can East Sicilians ,South Italian,and North Italian partitioned off.The different regions of Spain are subdivided as well.

grouping italians into one makes little sense since there are 5 groupings for Italians. There are 3 french groupings.
you seem to only have a justification of your claims to work by ONLY groupings these different genetic groups together. Clearly every paper on Italian genetics splits these groupings, that's what I have ever seen, but not you ..........what to do know something that others don't?

For your info, this is what I was given
North-italian ( Bergamo ) includes Swiss and Austrian-Tyrol
Tuscan
Abruzzo
South Italian
Sardinian

french are:
South-French
basque-French ( includes vasconic/aquitaria)
French

There 8 groupings and you place them into 2 ..........no wonder you do not make sense in claiming that WHG is more than ENF when you lump these groups together

Neo
01-20-2015, 07:41 PM
grouping italians into one makes little sense since there are 5 groupings for Italians.

This is my point why group all of these 5 groups into one or 3 groups into one ? It would be better to break them down ,that way we have clear readings on what the score for ancient components.





. Clearly every paper on Italian genetics splits these groupings, that's what I have ever seen, but not you ..........what to do know something that others don't?

??!!
Exactly,where did I say you should group all French and Italians into one?







There 8 groupings and you place them into 2 ..........no wonder you do not make sense in claiming that WHG is more than ENF when you lump these groups together


I think you misread my comment. My point was, it seems a bit peculiar that French and Italians are more shifted to ENF than WHG when comparing them with Balkan populations.You would expect the Balkan populations to be more ENF shifted.

I also found it strange that ENF was picked up Northern Europeans like Finns and Lithuanians on this spread,which according to some studies show no affinities to Near Easterners and are one of the untainted Northern Europeans.

lgmayka
01-20-2015, 09:47 PM
How much Basal Eurasian does Kostenki 14? I was reading that it's Y chromosome is of the haplogroup C, just like that of La Brana.Its more related to East Eurasian Y ---DNA and very distantly related to the C haplogroup in modern day Amerindians.
Not really. According to Table S6 in the the supplemental materials for the Kostenki paper (http://www.sciencemag.org/content/suppl/2014/11/05/science.aaa0114.DC1/Seguin-Orlando.SM.pdf), Kostenki-14 is F3393+ . C-F3393 (http://yfull.com/tree/C1/) is an early clade that eventually leads to C-V20 (http://yfull.com/tree/C1a2/) (European and Nepalese), C-M8 (http://yfull.com/tree/C1a1/) (Japanese), and C-F1370 (http://yfull.com/tree/C1b/) (South Asian).

The C-P39 in Native Americans is on a different branch of C called C-M217 (formerly known as C3). In fact, the closest relative to Native American C-P39 is C-F1756 (http://www.isogg.org/tree/ISOGG_HapgrpC.html), found in Poland, Kazakhstan, etc. (https://www.familytreedna.com/public/Chaplogroup/default.aspx?section=yresults)

Generalissimo
01-20-2015, 10:04 PM
French, Italians(Even Northern Italians) and Sicilians score higher Near East/ENF than Balkan populations(Bosnian,Croatian,Macedonian,Serbian ,etc), its a bit strange and not something one would expect. Italians,Sicilians,and French score over ~50- 60% which is around ~10-20% more than the Balkan populations. I also didn't expect for Finnish,Lithuanian, and Norwegian to have any ENF at all (lol), they score around 20% ENF from my general estimate.

You have some very strange expectations.

Of course most Balkan groups should have less ENF than Mediterranean groups. The former have very recent and considerable Slavic ancestry from the north.

And if Finns, Lithuanians and Norwegians didn't have any ENF at all (lol), then they'd be like Motala12 and other Scandinavian hunter-gatherers, which would be very strange indeed.

Neo
01-20-2015, 11:57 PM
You have some very strange expectations.

Of course most Balkan groups should have less ENF than Mediterranean groups. The former have very recent and considerable Slavic ancestry from the north.

And if Finns, Lithuanians and Norwegians didn't have any ENF at all (lol), then they'd be like Motala12 and other Scandinavian hunter-gatherers, which would be very strange indeed.

Would Balkans have more recent then the French who have Frankish ,Norse,and other post Iron Age ancestry from tribal groups, be any different? Seldin 2006,L.Kovaecevic et al 2014 and D.Shriner 2014 all desribe European populations having Northern European admixture and Southern European admixture at different levels depending on the region.They also describe French having a balanced amount of Southern European related and Northern European ancestry. L.Kovacevic (http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0105090)details Balkan populations registering more Near Eastern admixed than French.Shriner (http://www.nature.com/srep/2014/140813/srep06055/extref/srep06055-s1.pdf)picks up some ~10% Near Eastern in French. Southern European admixture could be very older in age than Northern European admixture,but there has been geneflow from South to North East Europe(see M.Nelis 2009) . The Southern European component is visibily strong in Southern European isolate populations like Sardinians and Basques.Point is ENF could hold components of Southern European from the Neolithic(non-Basal Eurasian components)



Not really. According to Table S6 in the the supplemental materials for the Kostenki paper (http://www.sciencemag.org/content/suppl/2014/11/05/science.aaa0114.DC1/Seguin-Orlando.SM.pdf), Kostenki-14 is F3393+ . C-F3393 (http://yfull.com/tree/C1/) is an early clade that eventually leads to C-V20 (http://yfull.com/tree/C1a2/) (European and Nepalese), C-M8 (http://yfull.com/tree/C1a1/) (Japanese), and C-F1370 (http://yfull.com/tree/C1b/) (South Asian).

The C-P39 in Native Americans is on a different branch of C called C-M217 (formerly known as C3). In fact, the closest relative to Native American C-P39 is C-F1756 (http://www.isogg.org/tree/ISOGG_HapgrpC.html), found in Poland, Kazakhstan, etc. (https://www.familytreedna.com/public/Chaplogroup/default.aspx?section=yresults)

Yea but at what frequency does C-V20? Its very rare. I think there was another European to carry C in Italy some where, I may be wrong.

Generalissimo
01-21-2015, 02:37 AM
Would Balkans have more recent then the French who have Frankish ,Norse,and other post Iron Age ancestry from tribal groups, be any different? Seldin 2006,L.Kovaecevic et al 2014 and D.Shriner 2014 all desribe European populations having Northern European admixture and Southern European admixture at different levels depending on the region.They also describe French having a balanced amount of Southern European related and Northern European ancestry. L.Kovacevic (http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0105090)details Balkan populations registering more Near Eastern admixed than French.Shriner (http://www.nature.com/srep/2014/140813/srep06055/extref/srep06055-s1.pdf)picks up some ~10% Near Eastern in French. Southern European admixture could be very older in age than Northern European admixture,but there has been geneflow from South to North East Europe(see M.Nelis 2009) . The Southern European component is visibily strong in Southern European isolate populations like Sardinians and Basques.Point is ENF could hold components of Southern European from the Neolithic(non-Basal Eurasian components).

The Shriner paper is based on a simple ADMIXTURE study. It's not informative about the real levels of Near Eastern and indigenous European ancestries because the components it shows are all recent composites.

Their Southern European component is certainly a mix of ENF, WHG and probably ANE, and so is their Northern European component, but in different proportions. The same goes for their Near Eastern component, but that probably has only a trivial amount of WHG, if any at all.

Btw, the levels of ENF across France and the Balkans vary a great deal. They're higher in southwestern France and the eastern Balkans, but much lower and close to Northern European levels in northern France and parts of Croatia and Slovenia.

lgmayka
01-21-2015, 04:16 AM
Yea but at what frequency does C-V20? Its very rare. I think there was another European to carry C in Italy some where, I may be wrong.
The C Haplogroup Project (https://www.familytreedna.com/public/Chaplogroup/default.aspx?section=yresults) shows C-V20 (or subclade C-V222) in
Germany
Spain
Poland
Ukraine
Hungary
Greece
Ireland
Scotland
England

parasar
01-21-2015, 05:56 AM
Yea but at what frequency does C-V20? Its very rare ...

~0% But frequency is not that important. It confirms the presence of this basal OoA lineage in Europe. And we cannot ascribe it to intensive testing. For example there is still no non-Roma (incld. one from Crete) L657 from Europe. Plus presence of C in K14, Hungary, La Brana.

Ebizur
01-21-2015, 09:41 AM
I think there was another European to carry C in Italy some where, I may be wrong.You probably are thinking of the individual from Italy in the study by Scozzari et al. 2012 in which C-V20 first has been defined. Those authors also have mentioned finding one additional instance of C-V20 in a sample from "southern Europe," but they have not indicated the provenance of that sample any more precisely than that.

Jean M
01-21-2015, 12:11 PM
~0% But frequency is not that important. It confirms the presence of this basal OoA lineage in Europe.

So now Y-DNA C1 (F3393) is a 'basal OOA' lineage because it was carried by one Palaeolithic man with some element of BE, though predominantly Western Eurasian UP? What about La Braña with no BE but the Y-DNA C1a2 (V20) that descends from C1? What about the descendants of C1 found in Japan?

What about the Neolithic EEF samples carrying a fraction of BE? Are all their mtDNA and Y-DNA haplogroups 'basal OOA'? The predominant Y-DNA signature of the European Neolithic is G2a. This seems most likely to have originated among Western Eurasian hunter-gatherers in the foothills of the Taurus/Zagros Mountains.

We might get solid proof of the Y-DNA signature predominant in BE if we ever get an ancient sample that is solidly BE. For the moment the most likely is Y-DNA E.

parasar
01-21-2015, 03:58 PM
~0% But frequency is not that important. It confirms the presence of this basal OoA lineage in Europe.


So now Y-DNA C1 (F3393) is a 'basal OOA' lineage because it was carried by one Palaeolithic man with some element of BE, though predominantly Western Eurasian UP? What about La Braña with no BE but the Y-DNA C1a2 (V20) that descends from C1? What about the descendants of C1 found in Japan?

What about the Neolithic EEF samples carrying a fraction of BE? Are all their mtDNA and Y-DNA haplogroups 'basal OOA'? The predominant Y-DNA signature of the European Neolithic is G2a. This seems most likely to have originated among Western Eurasian hunter-gatherers in the foothills of the Taurus/Zagros Mountains.

We might get solid proof of the Y-DNA signature predominant in BE if we ever get an ancient sample that is solidly BE. For the moment the most likely is Y-DNA E.

That is basal with a small b, nothing to do with the autosomal (so called) Basal Eurasian of Lazaridis which is limited to W. Eurasia.
I used basal in the sense that F3393 to me looks like an early and widespread Y lineage outside Africa as per its presence along the Atlantic (V20), the Pacific(M8), the Indian Ocean (M356), and in Oceania (M347) and Melanesia (M38).

Neo
01-21-2015, 04:06 PM
The Shriner paper is based on a simple ADMIXTURE study. It's not informative about the real levels of Near Eastern and indigenous European ancestries because the components it shows are all recent composites.

Their Southern European component is certainly a mix of ENF, WHG and probably ANE, and so is their Northern European component, but in different proportions. The same goes for their Near Eastern component, but that probably has only a trivial amount of WHG, if any at all.

Btw, the levels of ENF across France and the Balkans vary a great deal. They're higher in southwestern France and the eastern Balkans, but much lower and close to Northern European levels in northern France and parts of Croatia and Slovenia.

The Basque mostly cluster to Neolithic Swedish Farmers. Lithuanians are a good fit for Mesolithic Europeans.Sardinians are a good fit for ''Stuttgart''. There is evidence of genetic continuity from Mesolithic Swedish Hunter Gatherers to Neolithic Swedish Hunter Gatherers in populations like La Brana. Originally many Mesolithic Europeans had West Eurasian admixture of MHG(Mesolithic Hunter Gatherer), but later on MHG was supplanted and outmoded by WHG components(West Eurasian Hunter Gatherer) .WHG are what Loschbour and La Brana show affinities for. Loschbour,La Brana ,AJV(Pitted Ware Culture) and SF11 cluster to each other and are examples of genetic continuity Neolithic Swedish Hunter Gatherers from Mesolithic Swedish Hunter Gatherers . AJV and MA-1 cluster to each maybe because Ajv58 has ANE input. La Brana and Loschbour are less distant to Sardinians and Stuttgart, but share a bigger affinity to Ajv58 and SF11.


http://3.bp.blogspot.com/-hoBLZ0dZXto/U1luxCudqwI/AAAAAAAAJk4/J3X428YdPzo/s1600/PCA.png
'

MA-1 (Mal'-ta/Mesolithic Siberians) coincidently carried U5a1 like Ajv58 (Pitted Ware Culture) . We see the input of ANE and a related mt-DNA lineages U5a in the Ajv Samples (Pitted Ware) too. LA Brana is a good fit for Neolithic European Hunter Gathers and have affinity to Ajv58. The only difference is ''La Brana1/2'' are devoid of ANE.

The Y-DNA I2a1 is a is not found in Upper Paleolithic Europeans, but found in Mesolithic Europeans. Although I2a1 is rare in Scandinavians today , it probably was widespread in Mesolithic Europe, and existed from the Upper Paleolithic(I2a1 was found at least 2 samples of MA-1 and probably ended up in Scandanivia).I2a1 is more than likely a refugium clade that went to South-Western Europe during the LGM. After the Ice-Age, I2a1 became wide spread in West and Central Europe but never returned to high frequency Scandinavia. Coincidentally, the-mt-DNA U5a and U5b, are refugium subclades of the LGM.U5a or U5b are found in South-West Europe(Iberian peninsula) today.

Excuse me for being longwinded, but since La Brana are also very close to Neolithic Swedish Farmers who thus are close to Mesolithic Swedish farmers. Its safe to say, that Basques represent an archetype for untainted Europeans since they are in the same vicinity as La Brana. Its not likely they inherited geneflow from Early Neolithic Farmers that carried Near Eastern components. Other genetic studies,like L.Kovacevic 2014,corroborate French to have negligible Near Eastern ancestry,whether it be recent or from the Neolithic period.I propose that ENF is having a founder effect on many of the populations on this spread. Especially when Northern European populations like Lithuanians have amounts of ENF(Near Eastern ancestry).




Lazaridis et al 2014 (http://www.biorxiv.org/content/biorxiv/suppl/2014/04/02/001552.DC2/001552-3.pdf)


http://i.imgur.com/j9D3cnF.png


Loschbour groups with LaBrana, a Mesolithic Iberian huntergatherer5, into a Western European Hunter-Gatherer (WHG) cluster. Motala12 and Motala_merge are similar to each other and to Skoglund_HG a merge of Neolithic hunter-gatherers from Sweden6, thus forming a Scandinavian Hunter-Gatherer (SHG) cluster. The SHG appear intermediate between WHG and ANE, similar to the Global PCA and consistent with the evidence from f4-statistics (SI14).

Neo
01-21-2015, 04:14 PM
~0% But frequency is not that important. It confirms the presence of this basal OoA lineage in Europe. And we cannot ascribe it to intensive testing. For example there is still no non-Roma (incld. one from Crete) L657 from Europe. Plus presence of C in K14, Hungary, La Brana.

That is exactly my point,it seems to represent an OOA.Maybe at a time when C was more widespread through Eurasia.C3 is located in Siberia,moderate levels in East Asia and found in Oceania.C3 probably is a back migration from the Bering strait from America. C3 has been found in Na-Dene(who in which also carry ANE)and in South America at low frequencies.

parasar
01-21-2015, 04:33 PM
MA-1 (Motola/Mesolithic Russians) coincidently carried U5a1 like Ajv58 (Pitted Ware Culture) .

This is an error, perhaps typographical.

Neo
01-21-2015, 04:36 PM
This is an error, perhaps typographical.

Yes,thanks I just edited that.

Hando
01-21-2015, 04:46 PM
What about the Neolithic EEF samples carrying a fraction of BE? Are all their mtDNA and Y-DNA haplogroups 'basal OOA'? The predominant Y-DNA signature of the European Neolithic is G2a. This seems most likely to have originated among Western Eurasian hunter-gatherers in the foothills of the Taurus/Zagros Mountains.

We might get solid proof of the Y-DNA signature predominant in BE if we ever get an ancient sample that is solidly BE. For the moment the most likely is Y-DNA E.
So the WHG were originally from the Taurus/Zagros and carried G2a? Sorry, maybe I am confusing WHG with another group.

Neo
01-21-2015, 04:48 PM
From my view,Otzi ,Gok2 and Stuttgart retain Basal Eurasian and seem to be more of more shifted away from La Brana and Loschbour,not necessarily because they have Basal Eurasian but because they may have a slightly different admixture of West Eurasian(varying amounts of WHG and SHG).




http://2.bp.blogspot.com/-f0SM6wmjxww/U1lq1koSSwI/AAAAAAAAJks/_csA2iCuNGM/s1600/skoglund.png

So BEu has shown up K14 which is older than MA-1(Mal'ta).It's strange that during the Upper Paleolithic period , Basal Eurasian(BEu)shows up in smaller amounts in K14 sample,but in later periods during the Neolithic era of Europe, Basal Eurasian(BEu) shows up in Stuttgart at a higher volume than it did for K14 in the Upper Paloethic era .

Here's a passage I read from a website.

But this BEu component could not have come from the Middle East because modern Lithuanians are closer to K-14 than Stuttgart (Fig. S14), the alleged recipient of the Middle Eastern gene flow. So, the Middle Eastern populations must have received it from an UP European population related, first, to K-14, then to MA-1 and, finally, to Amerindians.


I half way agree with this, because modern Europeans are still very genetically drifted from the Basal Eurasian component.If BEu was from UP Europe ,it would be more widespread through out the continent in later years.

Generalissimo
01-21-2015, 10:49 PM
The Basque mostly cluster to Neolithic Swedish Farmers. Lithuanians are a good fit for Mesolithic Europeans.Sardinians are a good fit for ''Stuttgart''.

Some, maybe most, Sardinians are a good fit for Stuttgart. But Basques don't cluser with Neolithic Swedish farmers, and Lithuanians most certainly aren't a good fit for Mesolithic Europeans.

The main problem here is that you're using the projected positions of the ancient genomes to come to these conclusions. But you're not taking into account projection bias, which pushes these ancient samples closer to the middle of the plot.

Here's a plot from the Kostenki14 paper in which the authors made an effort to correct the results for projection bias. They did OK.

http://imageshack.com/a/img673/9131/528oyd.png

But here's a plot that doesn't suffer from projection bias at all, because none of the samples were projected.

http://imageshack.com/a/img907/9477/qC6VYf.png


Excuse me for being longwinded, but since La Brana are also very close to Neolithic Swedish Farmers who thus are close to Mesolithic Swedish farmers. Its safe to say, that Basques represent an archetype for untainted Europeans since they are in the same vicinity as La Brana. Its not likely they inherited geneflow from Early Neolithic Farmers that carried Near Eastern components.

La Brana-1 isn't very close to Swedish Neolithic farmers, since dimension 1 on the plots above carries a lot more variance than dimension 2. It's basically just a lower coverage version of Loschbour.

And Basques are indeed mostly of ENF and thus Near Eastern ancestry, although they do have a higher level of Western European Hunter-Gatherer (WHG) admixture than any southern Europeans. It's actually comparable to that in Northern Europeans, because their Ancient North Eurasian (ANE) admixture is lower.

Neo
01-22-2015, 01:30 AM
Some, maybe most, Sardinians are a good fit for Stuttgart. But Basques don't cluser with Neolithic Swedish farmers, and Lithuanians most certainly aren't a good fit for Mesolithic Europeans.

The main problem here is that you're using the projected positions of the ancient genomes to come to these conclusions. But you're not taking into account projection bias, which pushes these ancient samples closer to the middle of the plot.

Here's a plot from the Kostenki14 paper in which the authors made an effort to correct the results for projection bias. They did OK.

http://imageshack.com/a/img673/9131/528oyd.png

But here's a plot that doesn't suffer from projection bias at all, because none of the samples were projected.

http://imageshack.com/a/img907/9477/qC6VYf.png


La Brana-1 isn't very close to Swedish Neolithic farmers, since dimension 1 on the plots above carries a lot more variance than dimension 2. It's basically just a lower coverage version of Loschbour.

And Basques are indeed mostly of ENF and thus Near Eastern ancestry, although they do have a higher level of Western European Hunter-Gatherer (WHG) admixture than any southern Europeans. It's actually comparable to that in Northern Europeans, because their Ancient North Eurasian (ANE) admixture is lower.


http://imagizer.imageshack.us/a/img673/9131/528oyd.png

Belorussians , Lithiuianians , and Estonians are West Eurasians closest to the Mesolithic Swedish Hunter Gatherers
on the PCA. They still are closer to AJV.I also see the PCA repeating the same results for Basques, Basque are the closest modern day European population to Neolithic Europeans (LBR is virtually on the same dimension as LaBrana) and they are the closest modern day European population to La Brana.Basque also seem to be the modern Europeans closest to Loschbour. But the from the plot, you can see the Basque at a fulcrum point between Mesolithic European Hunter Gathers and Neolithic European Hunter Gatherers. Sardinians seem the best fit for Oetzi and Stuttgart for Neolithic Farmer Europeans. Basque are the most distant from Near Easterners on the PCA , although they plot with Neolithic Europeans who have Basal Eurasian, this kind of cements the idea that Basal Eurasian can't be Middle Eastern in origin.




http://imagizer.imageshack.us/a/img907/9477/qC6VYf.png

On this 2nd PCA, although Gok2 has basal Eurasian, Gok 2 still is a little repelled to Near Easterners and is more close to Southern Europeans. In fact, on this PCA Southern Europeans are closer to Near Easterners. Stuttgart are closer to Near Easterners than MA1 and Loschbour, but still Stuttgart are at a distance. So it convinces me that Basal Eurasian is not a Near Eastern component. The reality is this PCA does show Near Easterners and Caucasus strongly clustering with each other, so the PCA is actually giving a little bit of slack for Near Easterners.On other PCAs , although Near Easterners and Caucasus have an affinity to each other, there still is a small void between the two macro-populations.

Neo
01-22-2015, 02:35 AM
In summation, if Stuggart has more Near Eastern than the modern day Southern European, why doesn't it stream closer to Near Easterners than Southern Europeans do (on the 2nd PCA=? This is why things don´t seem to be adding up.

But if you take look at the first PCA, it does seem that Basque are intermediate between Mesolithic Scandanivian Hunter Gather and Neolithic Western European Hunter Gatherer.



http://eurogenes.blogspot.com/2014/12/ane-is-primary-cause-of-west-to-east.html


Stuttgart (Neolithic)

ANE 0
South_Eurasian 0
Near_Eastern 72.19
East_Eurasian 0
WHG 27.8
Oceanian 0
Pygmy 0
Sub-Saharan 0

Neo
01-22-2015, 02:53 AM
On this (http://imagizer.imageshack.us/a/img673/9131/528oyd.png) PCA,Kotesnki 14 is the only sample with Basal Eurasian that Middle Easterners have a slight affinity for.What you have to keep in mind , is that these Middle Eastern groups are outliers,such as Turks and Armenians.Which aren't true Middle Easterners at all. The rest of the ancient samples that seem to contain Basal Eurasian,like Oetzi,Stuttgart and Gok2 shift towards Sardinians and Southern Europeans to a lesser degree.

K14 seems to plot in the Middle of all these populations,whether they are ancient or modern populations. Whether they are European,Near Eastern, Caucasus, or Siberian. This makes sense, cause we know Kotesnki14 has Central Asian,South Asian,Siberian, African ,Middle Eastern and European components.

Jean M
01-22-2015, 10:52 AM
So the WHG were originally from the Taurus/Zagros and carried G2a? Sorry, maybe I am confusing WHG with another group.

WHG (European) is descended from Western Eurasian on the Lazaridis tree. Western Eurasian also contributed to EEF. See post above http://www.anthrogenica.com/showthread.php?3481-Basal-Eurasian-and-ASI-Split&p=59256&viewfull=1#post59256

Western Eurasian descends from "Western Eurasian UP" (Upper Palaeolithic) - see the tree in post http://www.anthrogenica.com/showthread.php?3481-Basal-Eurasian-and-ASI-Split&p=65196&viewfull=1#post65196

So Western Eurasian UP are the ancestral group (the first homo sapiens) who arrived in Europe, the Near East and North Africa in the Palaeolithic. At that stage they did not carry the Y-DNA haplogroups that appear in the Mesolithic, let alone the Neolithic. We have no Y-DNA from the Palaeolithic Near East, but we can deduce that what arrived there during the Palaeolithic was Y-DNA GHIJKLT and its descendant IJ. C1 had arrived in Europe by 40,000 years ago, but that may have by-passed the Near East.

3554

Generalissimo
01-22-2015, 12:14 PM
This makes sense, cause we know Kotesnki14 has Central Asian,South Asian,Siberian, African ,Middle Eastern and European components.

It doesn't really, it's just too old to be classified accurately in such modern terms.

But it is relatively closest to northern and eastern Europeans in formal tests like f3, f4 and D-stat, which is what really matters.

Neo
01-22-2015, 12:51 PM
WHG (European) is descended from Western Eurasian on the Lazaridis tree. Western Eurasian also contributed to EEF. See post above http://www.anthrogenica.com/showthread.php?3481-Basal-Eurasian-and-ASI-Split&p=59256&viewfull=1#post59256

Western Eurasian descends from "Western Eurasian UP" (Upper Palaeolithic) - see the tree in post http://www.anthrogenica.com/showthread.php?3481-Basal-Eurasian-and-ASI-Split&p=65196&viewfull=1#post65196

So Western Eurasian UP are the ancestral group (the first homo sapiens) who arrived in Europe, the Near East and North Africa in the Palaeolithic. At that stage they did not carry the Y-DNA haplogroups that appear in the Mesolithic, let alone the Neolithic. We have no Y-DNA from the Palaeolithic Near East, but we can deduce that what arrived there during the Palaeolithic was Y-DNA GHIJKLT and its descendant IJ. C1 had arrived in Europe by 40,000 years ago, but that may have by-passed the Near East.

3554

According to Lazirids 2014,WHG is posited to split from ANE and WHG ,24,000 years ago. ANE/WHG might of split from Eastern Non-Africans 40,000 years ago.


>24,000 years ago since this is the age6 of MA1 and this individual is on the ANE
lineage. The WHG must then have split from eastern non-Africans >40,000 years ago, as this is
the age of the Chinese Tianyuan sample which clusters with eastern non-Africans to the
exclusion of Europeans28.


It doesn't really, it's just too old to be classified accurately in such modern terms.

But it is relatively closest to northern and eastern Europeans in formal tests like f3, f4 and D-stat, which is what really matters.

Well yea, it really is too old too classify in modern terms. But ancient genomes, tend to be greatly polarized and create a definitive direction in which modern genomes to draw to. Take for example the MA-1 (Mal'ta) which are a good proxy for ANE, instead of MA-1 being an midpoint for Siberian populations, it tends to create a boundary line. Same instance with Loschbour and mot/Sweden, which are not a midpoint in modern populations, but create a polarity for modern European populations to pull by.


This is an error, perhaps typographical.

Actually the Ajivide are Pitter Ware Culture (http://www.sciencedirect.com/science/article/pii/S0278416514000117) in Gotland.

parasar
01-22-2015, 03:36 PM
WHG (European) is descended from Western Eurasian on the Lazaridis tree. Western Eurasian also contributed to EEF. See post above http://www.anthrogenica.com/showthread.php?3481-Basal-Eurasian-and-ASI-Split&p=59256&viewfull=1#post59256

Western Eurasian descends from "Western Eurasian UP" (Upper Palaeolithic) - see the tree in post http://www.anthrogenica.com/showthread.php?3481-Basal-Eurasian-and-ASI-Split&p=65196&viewfull=1#post65196

So Western Eurasian UP are the ancestral group (the first homo sapiens) who arrived in Europe, the Near East and North Africa in the Palaeolithic. At that stage they did not carry the Y-DNA haplogroups that appear in the Mesolithic, let alone the Neolithic. We have no Y-DNA from the Palaeolithic Near East, but we can deduce that what arrived there during the Palaeolithic was Y-DNA GHIJKLT and its descendant IJ. C1 had arrived in Europe by 40,000 years ago, but that may have by-passed the Near East.
...

That is not proven. Lazaridis too contemplated an alternative scenario whereby their Basal would be West Eurasian, their West Eurasian could be a returnee from the east.

the category “West Eurasian” could be transferred to the “basal Eurasian” element instead, as it is the only one whose presence we can detect only in West Eurasia, while the common ancestry of both MA1 and Loschbour with eastern non-Africans (drift non_African-->X) raises the alternative possibility of an eastern sojourn of their ancestors and a temporal priority of “basal Eurasians” in western Eurasia."

Hando
01-24-2015, 05:52 AM
WHG (European) is descended from Western Eurasian on the Lazaridis tree. Western Eurasian also contributed to EEF. See post above http://www.anthrogenica.com/showthread.php?3481-Basal-Eurasian-and-ASI-Split&p=59256&viewfull=1#post59256

Western Eurasian descends from "Western Eurasian UP" (Upper Palaeolithic) - see the tree in post http://www.anthrogenica.com/showthread.php?3481-Basal-Eurasian-and-ASI-Split&p=65196&viewfull=1#post65196

So Western Eurasian UP are the ancestral group (the first homo sapiens) who arrived in Europe, the Near East and North Africa in the Palaeolithic. At that stage they did not carry the Y-DNA haplogroups that appear in the Mesolithic, let alone the Neolithic. We have no Y-DNA from the Palaeolithic Near East, but we can deduce that what arrived there during the Palaeolithic was Y-DNA GHIJKLT and its descendant IJ. C1 had arrived in Europe by 40,000 years ago, but that may have by-passed the Near East.

3554

Thanks. It seems from the map that western Eurasian UP (ancestral group) arrived in Europe from the Near East (Taurus/Zagros) c 40,000BP? The map also has GHIJKLT migrating into Europe with these western Eurasian UP from the Near East c40,000BP. But does this mean G2 migrated with them during this time? Or with farmers during the Neolithic? I assumed the latter and therefore was confused by your comment about it being WHG. You said "The predominant Y-DNA signature of the European Neolithic is G2a. This seems most likely to have originated among Western Eurasian hunter-gatherers in the foothills of the Taurus/Zagros Mountains."

Jean M
01-24-2015, 11:52 AM
That is not proven. Lazaridis too contemplated an alternative scenario whereby their Basal would be West Eurasian, their West Eurasian could be a returnee from the east.

Let's not mix up geography and genes. On the map I gave, 'Western Eurasian UP' arrived in the Near East, Europe and North Africa from what I call the 'Asian crossroads', which would not be any specific point on the map, but hunter-gatherer bands milling around in Asia after an arrival via Arabia. These bands would not be strongly differentiated (if at all) one with another in the early days. Gradually, as they moved further apart, bands could become more isolated and develop genetic drift. When such bands first arrived in Western Eurasia, they would scarcely be much different from those bands which moved into East Asia. The "common ancestry of both MA1 and Loschbour with eastern non-Africans" is to be expected in this scenario. That's exactly what they had - common ancestry. What Lazaridis et al see as drift specific to modern East Asians could simply have been bred out of Western Eurasians. Or it could be the result of interbreeding while the bands were still milling around in Asia. I wouldn't care to be dogmatic about it.

If the component 'Basal Eurasian' represents a group that never entered Central Asia and simply remained in Arabia until forced to shift by climate change, then that would indeed give it the status of 'first group in the Near East (specifically Arabia) not to have any contact with people from any other part of the globe except Africa'. However if it left Arabia for Africa and only moved to the Levant in the Neolithic, then it actually started to have an input into the modern Western Eurasian gene pool in the Neolithic. The presence of Basal Eurasian in Kostenki 14 suggests that in reality some bands at the 'Asian crossroads' were travelling back and forth into Arabia. So it's not quite that clear-cut.

Jean M
01-24-2015, 11:54 AM
Thanks. It seems from the map that western Eurasian UP (ancestral group) arrived in Europe from the Near East (Taurus/Zagros) c 40,000BP?

No. I specified the foothills of the Taurus/Zagros Mountains as the place where farming first developed. That is not the same place as the Levantine UP sites on the map. This is all in AJ.


The map also has GHIJKLT migrating into Europe with these western Eurasian UP from the Near East c40,000BP. But does this mean G2 migrated with them during this time?

No, no, and no. The map does not say that at all. We can deduce that GHIIJKLT migrated into the Near East c. 47,000 BP from the Asian crossroads. GHIIJKLT (F1329/M3658/PF2622/YSC0001299, CTS2254/M3680/PF2657, FGC2045/Z12203) is the ancestral haplogroup that eventually gave birth to the later haplogroups of those labels. See http://www.isogg.org/tree/ISOGG_YDNATreeTrunk.html What exact Y-DNA haplogroup(s) went into Europe a thousand years later, we don't know, but we can say an ancient one or ones almost certainly not found in Europe today.



You said "The predominant Y-DNA signature of the European Neolithic is G2a. This seems most likely to have originated among Western Eurasian hunter-gatherers in the foothills of the Taurus/Zagros Mountains."

I have already explained to you that 'Western Eurasian hunter-gatherers' is not the same as WHG. WHG is a specific label used by Lazaridis et al 2014 for hunter-gatherers in Europe. There were also hunter-gatherers in the Near East. They shared a common ancestry with those in Europe. That common ancestry Lazaridis labelled 'Western Eurasian'. The ancestor of "Western Eurasian" is "Western Eurasian UP = the people we presume of the Levantine UP sites.

parasar
01-24-2015, 05:22 PM
Let's not mix up geography and genes. On the map I gave, 'Western Eurasian UP' arrived in the Near East, Europe and North Africa from what I call the 'Asian crossroads', which would not be any specific point on the map, but hunter-gatherer bands milling around in Asia after an arrival via Arabia. These bands would not be strongly differentiated (if at all) one with another in the early days. Gradually, as they moved further apart, bands could become more isolated and develop genetic drift. When such bands first arrived in Western Eurasia, they would scarcely be much different from those bands which moved into East Asia. The "common ancestry of both MA1 and Loschbour with eastern non-Africans" is to be expected in this scenario. That's exactly what they had - common ancestry. What Lazaridis et al see as drift specific to modern East Asians could simply have been bred out of Western Eurasians. Or it could be the result of interbreeding while the bands were still milling around in Asia. I wouldn't care to be dogmatic about it.

If the component 'Basal Eurasian' represents a group that never entered Central Asia and simply remained in Arabia until forced to shift by climate change, then that would indeed give it the status of 'first group in the Near East (specifically Arabia) not to have any contact with people from any other part of the globe except Africa'. However if it left Arabia for Africa and only moved to the Levant in the Neolithic, then it actually started to have an input into the modern Western Eurasian gene pool in the Neolithic. The presence of Basal Eurasian in Kostenki 14 suggests that in reality some bands at the 'Asian crossroads' were travelling back and forth into Arabia. So it's not quite that clear-cut.

I'm not mixing geography with genes, Lazaridis is. I'm happy to call the components k1, k2, k3. When Lazaridis et al. contemplate a "sojourn" of ancestors of West Eurasian and ANE to the east, it not just a special drift to the east but a population that went east and came back.

Anyway in my scenario, Basal is not necessarily related to Arabia. I think Basal is the layer which did not come into contact with Neanderthals.

Jean M
01-24-2015, 05:51 PM
I'm not mixing geography with genes, Lazaridis is. I'm happy to call the components k1, k2, k3.

I wasn't attempting to apportion blame either on you or Lazaridis, but simply saying that geographical labels are one thing, actual lines of descent are another. There is nothing in the 'alternative' view of Lazaridis that actually contradicts my view of the lines of descent.


When Lazaridis et al. contemplate a "sojourn" of ancestors of West Eurasian and ANE to the east, it not just a special drift to the east but a population that went east and came back.

I realise that for some people it is a matter of absorbing interest whether the ancestors of Y-DNA R spread north from a point east or west of South Asia, but it seems irrelevant to the main issue for European ancestry. So please hold me excused from trying to make up my mind on the matter, which I don't think I could do right now anyway.


I think Basal is the layer which did not come into contact with Neanderthals.

It could be. I've nothing against that idea, but it just seems like yet more pointless speculation in the absence of an aDNA sample of the proposed BE.

vettor
01-24-2015, 06:11 PM
No. I specified the foothills of the Taurus/Zagros Mountains as the place where farming first developed. That is not the same place as the Levantine UP sites on the map. This is all in AJ.



No, no, and no. The map does not say that at all. We can deduce that GHIIJKLT migrated into the Near East c. 47,000 BP from the Asian crossroads. GHIIJKLT (F1329/M3658/PF2622/YSC0001299, CTS2254/M3680/PF2657, FGC2045/Z12203) is the ancestral haplogroup that eventually gave birth to the later haplogroups of those labels. See http://www.isogg.org/tree/ISOGG_YDNATreeTrunk.html What exact Y-DNA haplogroup(s) went into Europe a thousand years later, we don't know, but we can say an ancient one or ones almost certainly not found in Europe today.



.

To further clarify your map , creation of haplogroups XNO along with P from K haplogroup on the modern border of Burma and India.

S haplogroup created where M is

I believe that from GHIJKLT, the split occurred a little earlier, GIJ split from HKLT before entering India.

Jean M
01-24-2015, 06:26 PM
See what happens when I am mad enough to put up a map with Y-DNA haplogroups on it? And all I wanted to do was explain the really very simple point that the men of the Levantine UP would not have carried the exact self-same Y-DNA SNPs as the people of the Near Eastern Neolithic 35,000 years later. (Because they were older. Because those SNPs hadn't occurred yet.) I should have posted a Y-DNA tree. :\

Somebody shoot me if I show signs of the same madness again. Or maybe some form of restraining order.

Neo
01-24-2015, 09:43 PM
Let's not mix up geography and genes. On the map I gave, 'Western Eurasian UP' arrived in the Near East, Europe and North Africa from what I call the 'Asian crossroads', which would not be any specific point on the map, but hunter-gatherer bands milling around in Asia after an arrival via Arabia. These bands would not be strongly differentiated (if at all) one with another in the early days. Gradually, as they moved further apart, bands could become more isolated and develop genetic drift. When such bands first arrived in Western Eurasia, they would scarcely be much different from those bands which moved into East Asia. The "common ancestry of both MA1 and Loschbour with eastern non-Africans" is to be expected in this scenario. That's exactly what they had - common ancestry. What Lazaridis et al see as drift specific to modern East Asians could simply have been bred out of Western Eurasians. Or it could be the result of interbreeding while the bands were still milling around in Asia. I wouldn't care to be dogmatic about it.


There were 1 or 2 admixtures that were present in Paleolithic Europeans , Mesolithic Hunter Gatherer (MHG) and Scandinavian Hunter Gatherer(SHG)the two maybe one in the same.Down the timeline, maybe during late Mesolithic or Neolithic periods, the convergence of WHG develops. WHG eventually engulfs MHG(Mesolithic Hunter Gather and/or Scandinavian Hunter Gatherer).



Lazaridis et al 2014
(http://www.biorxiv.org/content/biorxiv/suppl/2014/04/02/001552.DC2/001552-3.pdf)
European hunter-gatherers from Spain, Luxembourg, and Sweden fall outside
the genetic variation of West Eurasians in the direction of European differentiation from the Near
East, with a “West European Hunter-Gatherer” (WHG) cluster including Loschbour and La
Braña12, and a “Scandinavian Hunter-Gatherer” (SHG) cluster including the Motala individuals
and ~5,000 year old hunter-gatherers from the Swedish Pitted Ware Culture2. An “Early
European Farmer” (EEF) cluster includes Stuttgart, the ~5,300 year old Tyrolean Iceman19 and a
~5,000 year old southern Swedish farmer2, and is near present-day Sardinians2,19

http://1.bp.blogspot.com/-jlF6eSOWmnk/VFwpvCk9MjI/AAAAAAAAJ1o/lkmfDp204OU/s1600/F2.large.jpg


If the component 'Basal Eurasian' represents a group that never entered Central Asia and simply remained in Arabia until forced to shift by climate change, then that would indeed give it the status of 'first group in the Near East (specifically Arabia) not to have any contact with people from any other part of the globe except Africa'. However if it left Arabia for Africa and only moved to the Levant in the Neolithic, then it actually started to have an input into the modern Western Eurasian gene pool in the Neolithic. The presence of Basal Eurasian in Kostenki 14 suggests that in reality some bands at the 'Asian crossroads' were travelling back and forth into Arabia. So it's not quite that clear-cut.

Kotesnki 14 had 5 basic admixtures which were Middle Eastern,Central Asian, East Asian ,Sub Saharan ,Basal Eurasian and South Asian. It would be nearly impossible for K14s ethnic group to be on a prehistoric world tour in these regions and interbred with the locals so fast. Not to mention the differentiation in linguistics,which would of made a language barrier in Eurasia between different ethnicities. Its possible that K14 could represent a archaric Eurasian ethnic group that later would have its descendants dispersed through out Middle East ,Central Asia,East Asia and Europe .But I think it might be so old that it represents a time Ancient Non Africans were genetically the same but later their alleles and SNPs became more speciated. K14 could be a perfect fit for West Eurasian UP.

Jean M
01-24-2015, 10:05 PM
Kotesnki 14 had 5 basic admixtures which were Middle Eastern,Central Asian, East Asian ,Sub Saharan ,Basal Eurasian and South Asian. It would be nearly impossible for K14s ethnic group to be on prehistoric world tour in these regions and interbred with the locals so fast. ... I think it might be so old that it represents a time West Eurasians were genetically the same but later their alleles and SNPs became more speciated. K14 could be a perfect fit for West Eurasian UP.

I agree with you on general principles i.e. that we shouldn't judge ancient samples by comparison with modern populations. Homo sapiens samples as ancient as 40,000 years ago will be less differentiated one from another than later populations. I'm not sure that Kostenki 14 will prove to be an exact fit for the Levantine UP, which I'm guessing carried mtDNA U. Kostenki 14 is thousands of years younger and carried U2, which makes it likely that his ancestors (at least on the maternal side) broke away from the 'Asian crossroads' several thousand years later than those who arrived in the Levant (I think) carrying mtDNA U. Certainly he is part of the UP mix in Europe though.

vettor
01-24-2015, 10:43 PM
See what happens when I am mad enough to put up a map with Y-DNA haplogroups on it? And all I wanted to do was explain the really very simple point that the men of the Levantine UP would not have carried the exact self-same Y-DNA SNPs as the people of the Near Eastern Neolithic 35,000 years later. (Because they were older. Because those SNPs hadn't occurred yet.) I should have posted a Y-DNA tree. :\

Somebody shoot me if I show signs of the same madness again. Or maybe some form of restraining order.

map is fine, just missing some things..............basically nearly same as mine...............but I have persian gulf as a river/s system - pre flooding era. (the garden of eden scenario around modern basra )

My gun got stolen, sorry

Neo
01-25-2015, 01:45 AM
I agree with you on general principles i.e. that we shouldn't judge ancient samples by comparison with modern populations. Homo sapiens samples as ancient as 40,000 years ago will be less differentiated one from another than later populations. I'm not sure that Kostenki 14 will prove to be an exact fit for the Levantine UP, which I'm guessing carried mtDNA U. Kostenki 14 is thousands of years younger and carried U2, which makes it likely that his ancestors (at least on the maternal side) broke away from the 'Asian crossroads' several thousand years later than those who arrived in the Levant (I think) carrying mtDNA U. Certainly he is part of the UP mix in Europe though.

Also we can't forget that haplogroups and subclades don't always mesh well with ancient components. We see this with E-M81 in Maghrebs whose paternal subclade emerged around 20,000 years ago, their ACs emerged 24kya. I am not saying Kotesnki 14 would be an exact fit for Levantine,but he might very well be a forerunner for the Levantine Eurasians.K14 has nearly all modern ACs according to testing, so k14 must represent a people who maybe the part of parent Macro-Eurasian group(or part of it).

Jean M
01-25-2015, 11:05 AM
I am not saying Kotesnki 14 would be an exact fit for Levantine, but he might very well be a forerunner for the Levantine Eurasians.

If you mean forerunner for Levantine Upper Palaeolithic (the source for the main flow into European UP), what I'm saying is that Kostenki 14 was not the forerunner. Kostenki 14 was thousands of years younger i.e. a later departure from the Asian crossroads than the Levantine UP and the first Homo sapiens in Europe.

The Ust'Ishim man from western Siberia is earlier (45,770–44,010 cal BP). He represents an OOA population prior to the split into East Asian and Western Eurasian. So he would be rather closer to the first Homo sapiens to arrive in the Levant and Europe. It doesn't make a huge difference, but I'm just pointing it out for the avoidance of any confusion.

Neo
01-25-2015, 06:06 PM
If you mean forerunner for Levantine Upper Palaeolithic (the source for the main flow into European UP), what I'm saying is that Kostenki 14 was not the forerunner. Kostenki 14 was thousands of years younger i.e. a later departure from the Asian crossroads than the Levantine UP and the first Homo sapiens in Europe.

The Ust'Ishim man from western Siberia is earlier (45,770–44,010 cal BP). He represents an OOA population prior to the split into East Asian and Western Eurasian. So he would be rather closer to the first Homo sapiens to arrive in the Levant and Europe. It doesn't make a huge difference, but I'm just pointing it out for the avoidance of any confusion.

To explain it from another ange,is that k14 may represent a genetic monotone of Upper Paloelithic Eurasians in the Upper Paleolithic. K14 couldn't of been part of the OOA migration, that would be absurd, since its 36,000 years old,but it may very well be indicative that Upper Paleolithic humans couldn't of been that far diverged from one another.It wouldn't be a bad speculation if we say that haplogroup C was common in Europe during the UP(since it survived from the La Brana in the Neolithic and k14 ). K14 has every global AC, except for Amerindian(which is because Amerindian may have descended from an endogamous group in Siberia), the African components remaining in K14 is by chance a cauasation of it taking a long period of time for genetic drift to occur and its ancestors hadn't been out of Africa long enough.Like I said its not likely that K14 ancestors are the result of hybrid of people all over. Making it from the vicious frigid Siberia, to moonsons of South Asia and then East Asia(crossing deserts and mountains) when taking into account the window period of OOA migration, would of been impossible.By some estimates humans were in East Asia by 30kya and Europe 40 kya. The first successful OOA migration is to be 75000 years ago.

Neo
01-25-2015, 07:23 PM
According to Cristina Gamba et al 2014 (http://www.nature.com/ncomms/2014/141021/ncomms6257/pdf/ncomms6257.pdf) , Haplogroup C survives into the Neolithic with the samples NE5 and NE6.But aformentioned samples look similar to Stuttgart.

http://i.imgur.com/AJrlnic.png

Neo
01-27-2015, 04:23 AM
I was looking at Lazaridis et al,and I tried to pinpoint the Basal Eurasian admixture observed in the aDNA of Stuttgart to the other modern populations today. Take a look at the light blue admixture,most Africans seem to have this admixture ,every population in this K run shows traces of THIS including Africans. Its not just isolated African groups like the Horners that have this bluish cluster, this admixture is present even in the case of Southern Africans.Khoisan populations like the Nama and the Khomani seem to have this ice bluish admixture, but Ju Hoan seem to be absolvent of it.

Look at page 33 (http://arxiv.org/ftp/arxiv/papers/1312/1312.6639.pdf) of Lazaridis et al 2014.


http://i.imgur.com/PWehQDk.png?1


http://i.imgur.com/bxAVFJs.pnghttp://i.imgur.com/4ejvpi1.png



According to Lazaridis Basal Eurasian looks like a good fit for the Y-DNA haplogroup E.



Lazaridis (http://arxiv.org/ftp/arxiv/papers/1312/1312.6639.pdf)


Finally, it could reflect continuing more recent gene
flows between the Near East and nearby Africa after the initial out-of-Africa dispersal, perhaps
associated with the spread of Y-chromosome haplogroup E subclades from eastern Africa11,12 into the
Near East, which appeared at least 7,000 years ago in Neolithic Europe13, or the detection of African
skeletal morphology in Epipaleolithic Natufians from Israel14.






More speculatively, some basal Eurasian admixture in the Near East may reflect the
early presence of anatomically modern humans9 in the Levant, or the populations responsible for the
appearance of the Nubian Complex in Arabia10, both of which date much earlier than the widespread
dissemination of modern humans across Eurasia.



Stuggart is dated to 7,000 years ago,we know that some subclades of E-78 (V13,V22 ,and V65)found in Europe fit the window of 7,000 years ago.These subclades could of migrated to the Balkans and carrying Basal Eurasian. See Cruciani et al. 2007 and Steven Bird et al. 2007 who go into the migration and origin of these subclades.


S Bird et al 2007
(http://www.jogg.info/32/bird.pdf)

The Origins of the British, Stephen Oppenheimer (2006) advanced a theory of a Neolithic time period for the arrival of E3b (and a companion haplogroup, J2) in Britain,2 corresponding to the period from 6.5-5.5 kya (thousands of years ago) and originating from the Balkan peninsula.3


S.Bird agrees with E3b1 found in Europeans to be associated with LBK culture of the Neolithic.


S Bird et al 2007
(http://www.jogg.info/32/bird.pdf)

haplogroups E3b and J in western Europe during the Neolithic era, but did not include any data from the island of Britain specifically, and upon the earlier work of Ammerman and CavalliSforza (1984) concerning the “demic diffusion” model, in which the Linearbandkeramik or LBK culture arose after the Neolithic transition (with the Starčevo-Körös- Çris cultures) about 6000 BCE or 8 kya.


According to a conducted test,the subclade of E called E-V13, peaks in Kosovar Albanians at 43% and is found in some Germans at ~3-4% by frequency in some samples, but most geneticist agree it entered Europe through the Balkans during late Neolithic. Cruciani et al 2007 dates V13 around 18kya -5.9 kya.Some of their estimates into Europe date 5kya-7kya.



Cruciani et al 2007
(http://mbe.oxfordjournals.org/content/24/6/1300.full)

The nested arrangement of haplogroups E-V12 and E-V32 defines an upper and lower bound for this episode, that is, 18.0 ky and 5.9 ky, respectively.


Several lines of evidence suggest that E-M78 subhaplogroups E-V12, E-V22, and E-V65 have been involved in trans-Mediterranean migrations directly from Africa.







Cruciani et al 2007
(http://mbe.oxfordjournals.org/content/24/6/1300.full)

Haplogroup E-V13 is the only E-M78 lineage that reaches the highest frequencies out of Africa. In fact, it represents about 85% of the European E-M78 chromosomes with a clinal pattern of frequency distribution from the southern Balkan peninsula (19.6%) to western Europe (2.5%). The same haplogroup is also present at lower frequencies in Anatolia (3.8%), the Near East (2.0%), and the Caucasus (1.8%).

Neo
01-27-2015, 06:38 AM
In accordance with E3b1 (v12,V13,V22,v32and V65) migration from Africa into Europe possibly being part of the population that carried Basal Eurasian and K14 carrying Basal Eurasian that was part of C haplogroup (which may be part of the original CT Out of Africa migration),we can stipulate that the Basal Eurasian component found in these ancient genomes(K14 and Stuttgart) are the result of successive waves out of Africa. And there couldn't of been too much of a time lapse for the migration of Stuttgart and K14 ancestors out of Africa .I’m scratching my head as to why Stuttgart and Otzi have Basal Eurasian admixture at higher amounts during later periods(5,000-7000 years ago) in contrast to K14 36,000 years ago. One could hypothesize, that Basal Eurasian is part of an ambiguous genetic substructure that has to be dissected with more prudent genetic testing methods. I think Basal Eurasian is an outer layer of the original African components between the different Macro-Eurasian admixtures. K14 seems to have an affinity for every modern AC (with the exception of Amerindian), which maybe a hint of how Out of African populations took a long time to become distinguished from each other genetically.

Neo
02-01-2015, 02:57 AM
La Brana does have some minor Basal Eurasian. This might hint that La Brana had some ancestry from Early European Farmers. The yellow lines from Stuttgart that contact the lines connected to Mbuti may signify that Stuttgart and La Brana have ancestors that derived from contemporaries of the Mbuti or a population similar to them. This is a another example of Basal Eurasian affinity to African populations.





http://i.imgur.com/IpI6UIo.png

http://i.imgur.com/4KZZr40.png




^^^^Above

On the Eurogenes Treemix the Hadza show geneflow into Stuttgart,maybe this is representative of how archaic the Basal Eurasian component is before it transitioned to other Eurasian components such as the macro-admixtures West Eurasian, Ancient South Eurasian, and East Eurasian. Stuttgart seems to be receiving gene flow from African populations,there is a similar pattern shown in Lazaridis et al Supplemental 2014.

pg 139-144 Lazaridis et al 2014
(http://arxiv.org/ftp/arxiv/papers/1312/1312.6639.pdf)


http://i.imgur.com/lStu8dW.png

http://i.imgur.com/QW7UBFU.png



^^^Above

You can also notice that MA1 contacts to the lines that are connected Karitiana and Motola12.Also notice that Iceman seems to be indirectly connnected to Mbuti by a line running adjacent to Stuttgart,which means that the Iceman ancestors may have recieved Basal Eurasian from an ethnic group belonging to the Stuttgart sample.


http://i.imgur.com/CMwJhLa.png


^^^Above

With this TreeMix chart above, there are lines from Iceman ,Stuttgart, and La Brana that adjoin the line stemming from Mbuti. Which represent some geneflow from Mbuti to Iceman ,Stuttgart and to a lesser extent La Brana.This is because La Brana has a minor amount of Basal Eurasian.


This is below are TreeMix charts from Eurogenes (http://eurogenes.blogspot.com/2014/11/treemix-graphs-with-kostenki14-and-ust.html)which show Hadza ethnic group genetic connection to the Stuttgart sample.








http://i.imgur.com/mcPtg1N.png

http://i.imgur.com/OHMttvW.png

With the 2 treemix charts above we see that Stuttgart has geneflow indirectly to Horner populations Ethiopian and Somali while it is also shows direct geneflow to the Hadza.


http://i.imgur.com/8WgNARi.png

http://i.imgur.com/9gPdQd2.png



Lazaridis et al 2014 Supplemental
(http://arxiv.org/ftp/arxiv/papers/1312/1312.6639.pdf)

When we allow three migrations (Figure S16.4), we observe an extra Basal Eurasian migration edge into LaBrana (17%) as well as MA1 admixture into Karitiana (39%) and Basal Eurasian admixture into Stuttgart (52%) with the remainder (48%) from the (Loschbour, LaBrana) common ancestor

When we allow four migrations (Figure S16.4), there is 44% Basal Eurasian admixture into Stuttgart with the remainder 56% of Stuttgart’s ancestry from the ((Loschbour, LaBrana), Motala) common ancestor. We also observe 41% of MA1 admixture into Karitiana, 15% Basal Eurasian admixture into LaBrana, and a new admixture from MA1 into Motala (11%). As mentioned above, we do not find compelling evidence that LaBrana and Loschbour differ in their relationship to eastern non-Africans using a formal D-statistic test.

parasar
02-01-2015, 05:45 AM
If you mean forerunner for Levantine Upper Palaeolithic (the source for the main flow into European UP), what I'm saying is that Kostenki 14 was not the forerunner. Kostenki 14 was thousands of years younger i.e. a later departure from the Asian crossroads than the Levantine UP and the first Homo sapiens in Europe.

The Ust'Ishim man from western Siberia is earlier (45,770–44,010 cal BP). He represents an OOA population prior to the split into East Asian and Western Eurasian. So he would be rather closer to the first Homo sapiens to arrive in the Levant and Europe. It doesn't make a huge difference, but I'm just pointing it out for the avoidance of any confusion.

That is not the case, had that been the case Ust-Ishim would be equally close to Europeans and E. Asians.

Skyfall
09-28-2015, 07:47 PM
What is ASI composed of? What does it split into? What % of it is West Eurasian? And how is it related to the "South Indian" component on Harappa?

Shaikorth
09-28-2015, 08:25 PM
That is not the case, had that been the case Ust-Ishim would be equally close to Europeans and E. Asians.

I think Jean is going for only ANE and WHG being original West Eurasian.

@Skyfall

ASI is a theoretical construct that's supposed to be the East Eurasian part of South Indian and not West Eurasian at all. Can be proxied with Dai in methods based on formal testing like f4-stats.

Skyfall
09-29-2015, 10:04 PM
Thanks so much Shaikorth! Could you expand on two things for me?

1) What does the "South Indian" component of Harappa break down into? Is it a 50/50 split between Western and Eastern Eurasian? For instance, if a caste like the "Bhatia" are 25% South Indian, would it be fair to say that since 50% of the South Indian component is Western Eurasian in ancestry, then the Bhatia are 12.5% ASI/East Eurasian and 12.5% Western Eurasian, giving us a total of 75+12.5 = 87.5% West Eurasian? I'd appreciate it if you could offer me your perspective on this calculation.

2) When you say that ASI can be proxied with Dai in methods based on formal testing i.e F4-stats, are you saying that ASI is mostly Eastern Eurasian in nature and not more closely related to the Onge? In other words, that ASI is more related to Dai than it is to the Onge? I've read conflicting opinions on this matter, and would greatly be indebted to you if you could clarify this issue for me. What is ASI exactly, and what ancestral and modern day population is it most closely related to?

Shaikorth
09-30-2015, 06:54 AM
1) What does the "South Indian" component of Harappa break down into? Is it a 50/50 split between Western and Eastern Eurasian?



Can't really say. Other posters here have looked into Harappaworld component breakdowns more than I have.




2) When you say that ASI can be proxied with Dai in methods based on formal testing i.e F4-stats, are you saying that ASI is mostly Eastern Eurasian in nature and not more closely related to the Onge? In other words, that ASI is more related to Dai than it is to the Onge? I've read conflicting opinions on this matter, and would greatly be indebted to you if you could clarify this issue for me. What is ASI exactly, and what ancestral and modern day population is it most closely related to?


ASI is some kind of East Eurasian. Thanks to drift it isn't identical to either Onge or Dai. In the TreeMix test below (thanks to Polako for that) you can see a 31% migration edge to Kalash from the East Eurasian branch - note that it comes from the root branch and not from an individual population like Dai. That's mostly caused by ASI, though since the East Eurasian branch has Ulchi there likely are other factors like ANE involved, pure ASI in Kalash shouldn't be as high as 31%.

http://oi59.tinypic.com/6yz0y0.jpg

DMXX
09-30-2015, 07:55 AM
ASI is some kind of East Eurasian. Thanks to drift it isn't identical to either Onge or Dai. In the TreeMix test below (thanks to Polako for that) you can see a 31% migration edge to Kalash from the East Eurasian branch - note that it comes from the root branch and not from an individual population like Dai. That's mostly caused by ASI, though since the East Eurasian branch has Ulchi there likely are other factors like ANE involved, pure ASI in Kalash shouldn't be as high as 31%.


How much ANE do the Ulchi typically have? If the ANE is subsumed by this signal, I would assume it's higher than Afanasievo and Yamnaya, given Neolithic steppe populations possess nowhere near as much as South-Central Asians tend to (usually seems to be a 10+% difference).

Generalissimo
09-30-2015, 08:22 AM
Ulchi have around 10% of ANE. Much less than most Siberians, and about the same as Nganasans.

The 30-40% migration edges to the Kalash that show up regularly in such TreeMix runs are a mystery at the moment. They're probably a mixture of various things, such as Dai-like ASI ancestry, as well as ANE and other stuff from Central and maybe even West Asia. That's why the root of the edge is shifted away from the East Asians.

The only way around this problem is to run some samples from Neolithic Turkmenistan, Uzbekistan, Pakistan and/or Afghanistan.

Shaikorth
09-30-2015, 08:23 AM
How much ANE do the Ulchi typically have? I would assume it's higher than Afanasievo and Yamnaya, given Neolithic steppe populations possess nowhere near as much as South-Central Asians tend to (usually seems to be a 10+% difference).

Ulchis are Southeast Siberians, so their ANE likely isn't as high as South-Central Asians either. The exact number will vary depending on the method used. Flegontov et al. got 30% for Nganasans using f4 ratio and Dai as ENA reference, I doubt Ulchis would get higher than that, in fact they might get a bit less.

Edit. checked the Flengontov tests again and it's in fact clear that Nganasans have more ANE than Ulchis (Southern Tungusics) and Oroqens (Northern Tungusics). Using either of these ANE-mixed groups as ENA references in a f4 ratio test still resulted in a successful tests with Nganasans getting MA-1 related ancestry.

Gravetto-Danubian
09-30-2015, 08:48 AM
I was looking at Lazaridis et al,and I tried to pinpoint the Basal Eurasian admixture observed in the aDNA of Stuttgart to the other modern populations today. Take a look at the light blue admixture,most Africans seem to have this admixture ,every population in this K run shows traces of THIS including Africans. Its not just isolated African groups like the Horners that have this bluish cluster, this admixture is present even in the case of Southern Africans.Khoisan populations like the Nama and the Khomani seem to have this ice bluish admixture, but Ju Hoan seem to be absolvent of it.

Look at page 33 (http://arxiv.org/ftp/arxiv/papers/1312/1312.6639.pdf) of Lazaridis et al 2014.



According to Lazaridis Basal Eurasian looks like a good fit for the Y-DNA haplogroup E.






Stuggart is dated to 7,000 years ago,we know that some subclades of E-78 (V13,V22 ,and V65)found in Europe fit the window of 7,000 years ago.These subclades could of migrated to the Balkans and carrying Basal Eurasian. See Cruciani et al. 2007 and Steven Bird et al. 2007 who go into the migration and origin of these subclades.


S.Bird agrees with E3b1 found in Europeans to be associated with LBK culture of the Neolithic.


According to a conducted test,the subclade of E called E-V13, peaks in Kosovar Albanians at 43% and is found in some Germans at ~3-4% by frequency in some samples, but most geneticist agree it entered Europe through the Balkans during late Neolithic. Cruciani et al 2007 dates V13 around 18kya -5.9 kya.Some of their estimates into Europe date 5kya-7kya.


Not to diss your efforts, but what does Bird's hypothesis reaching England via Ramano-Balkan soldiers prove exactly ?
-of EV13, that is

bored
11-06-2015, 10:22 AM
If you mean forerunner for Levantine Upper Palaeolithic (the source for the main flow into European UP), what I'm saying is that Kostenki 14 was not the forerunner. Kostenki 14 was thousands of years younger i.e. a later departure from the Asian crossroads than the Levantine UP and the first Homo sapiens in Europe.

The Ust'Ishim man from western Siberia is earlier (45,770–44,010 cal BP). He represents an OOA population prior to the split into East Asian and Western Eurasian. So he would be rather closer to the first Homo sapiens to arrive in the Levant and Europe. It doesn't make a huge difference, but I'm just pointing it out for the avoidance of any confusion.

This is what I believe as well. How is Ust'Ishim ASI? It doesn't make sense. The reason it is closer to East Asians is because it lacks Basal Eurasian.

epoch
11-06-2015, 06:41 PM
Also we can't forget that haplogroups and subclades don't always mesh well with ancient components. We see this with E-M81 in Maghrebs whose paternal subclade emerged around 20,000 years ago, their ACs emerged 24kya. I am not saying Kotesnki 14 would be an exact fit for Levantine,but he might very well be a forerunner for the Levantine Eurasians.K14 has nearly all modern ACs according to testing, so k14 must represent a people who maybe the part of parent Macro-Eurasian group(or part of it).


If you mean forerunner for Levantine Upper Palaeolithic (the source for the main flow into European UP), what I'm saying is that Kostenki 14 was not the forerunner. Kostenki 14 was thousands of years younger i.e. a later departure from the Asian crossroads than the Levantine UP and the first Homo sapiens in Europe.

The Ust'Ishim man from western Siberia is earlier (45,770–44,010 cal BP). He represents an OOA population prior to the split into East Asian and Western Eurasian. So he would be rather closer to the first Homo sapiens to arrive in the Levant and Europe. It doesn't make a huge difference, but I'm just pointing it out for the avoidance of any confusion.

If you take a look at paleolithic classification one of the things that is so striking is that while the Gravettian, Solutrean or Magdalenian are pretty much well defined, the Aurignacian is divided in a lot of sub timeframes. These timeframes, subcultures are not very well defined and keep changing. Did we at first have a Perigordian and an Early, Middle and Late Aurignacian, we now have a Pre-Aurignacian and a Proto-Aurignacian. A number archaeologists have the Early Aurignacian subdivided in a number of (sub-)cultures. Take for instance a look at John Hawks description of the Kostenki complex:

http://johnhawks.net/weblog/reviews/archaeology/upper/vishnyatsky_2004_kostenki.html

Considering that Oase 1 and Kostenki 14, while not exactly contemporary still quite close to each other in age, look utterly unrelated to each other in the D statistics, and also considering that Kostenki 14 has Basal Eurasian pointing possibly to contact with other groups, I think the first AMHs in Europe were more than one group, but several different peoples living alongside of each other. Intermingling but still very much distinct.

Also, possibly coming from more than one direction. While nowadays the Caucausus may serve as a barrier during several periods of the ice age larger part of the flats before the coastline now under water were laid bare and could be traveled easily. Sicily was at one point separated from Africa by only a small straight. If U5b1b1 can travel to Berbers and Saami, and Proto-Aboriginals manage to cross the Wallace line, why wouldn't early European AMHs be able to cross over to Sicily?

If they will extract nuclear DNA from Fumane 2 that would prove to be interesting.

parasar
11-06-2015, 07:18 PM
This is what I believe as well. How is Ust'Ishim ASI? It doesn't make sense. The reason it is closer to East Asians is because it lacks Basal Eurasian.

Ust-Ishim is 45000 years old. That is the time ASI ancestors split. So Ust-Ishim at 45000 year old is essentially the type of ASI that existed at that time.
The reason he is closest (slightly but not significantly) to the Ongee is because Ongee have stayed isolated for long, and he was just slightly on the Ongee side of the split.

http://3.bp.blogspot.com/-VaHQZo9wITM/VEf9tMQhktI/AAAAAAAAJ00/aRlFR-Z6Nts/s1600/nature13810-f3.jpg

Ust's IBD centroid lies somewhere in Burma perhaps not very far from where CTS11667,Z4842/M2308 originated. But no matter where the ASI split occurred, no other Eurasian was very different at that time from him and the ancestors of the Ongee since there is a 50000year OoA bottleneck.

"Malaysian Chr Y sequence data (Wong et al. 2013) reveals a split in
haplogroup F that predates the G/HT split by one mutation, F1329 (Figure S13). This finding is
in accordance with the two Lahu F2-M427 individuals reported in Poznik et al. (2013) as having
an ancestral allele of M578. In combination with the presence of deep branches of K in Southeast
Asia, this further strengthens the model proposing that the initial radiation of the non-African
Chr Y lineages may have taken place somewhere in Southeast Asia (Karafet et al. 2014).
Following PhyloTreeY (van Oven et al. 2014) we re-define the internal structure of haplogroup
H-M3035 that now incorporates South Asian lineages H1-M69 (predominantly found in Indian
peninsula), H2-B108 (detected in one of our Burmese samples) and H3-Z5857 (India) that
previously (Karafet et al. 2008) were recognized as F* (Figure S23). Although all F* lineages
from South Asia in our data belong to H the phylogenetic depth (40-44 kya) of its division into
three primary subclades suggests that their distribution patterns may also be considered
informative about the process of initial radiation of non-African Y chromosomes (Figure S9).
Although absent in 728 South Asian samples (Sengupta et al. 2006) the rare H4-M282/P96
lineage (van Oven et al. 2014) has been observed in two Iranians (Regueiro et al. 2006), one
French (Poznik et al. 2013) and one Dutch individuals (Karafet et al. 2008) as well as several
low coverage Sardinian sequences (Francalacci et al. 2013). Intersecting the Sardinian variants
with our data allows us to approximately position the H4 lineage within haplogroup H (Figure
S23)...

haplogroups G and IJ have their spread restricted predominantly to West
Eurasia, H is restricted to South Asia, and only the newly defined F2 branch is potentially
restricted to Southeast Asia. Considering the geographic distribution of the F, C, D derived
clades in combination with the four primary subclades of K, overall, the Chr Y data appear to
support the model by which the initial radiation of non-African genetic diversity was a rapid
process involving almost simultaneous splits of the ancestors of West and East Eurasian, as well
as Oceanian populations
...
we map the position of the F2 clade represented by Malay sample SSM072 and redefine haplogroup NO by F549 and 4
equivalent mutations. NO splits further into NO1-M214 and the novel NO2-F2755, as
defined by the SSM016 sequence."
http://genome.cshlp.org/content/suppl/2015/02/18/gr.186684.114.DC1