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Twilight
16-09-16, 16:43
So apparently according to the new Mtdna X Page, Mtdna N1,N2,X and W were considered Basal Eurasian Haplogroups. Yet it appears that Mtdna N1,N2,X and W were dominate in early farmers/Natufians. Is Maciamo saying that the Natufians culture was 100% Basal Eurasian?
http://www.eupedia.com/europe/Haplogroup_X_mtDNA.shtml
http://cdn.eupedia.com/images/content/8000BCE-haplogroups.png

IronSide
06-02-18, 18:09
I wonder if Basal Eurasians left only their mtDNA as proof of their existence ... maybe they were a female dominated culture, it doesn't seem that the Basal in Iran Neolithic and Natufians were that much differentiated and they existed in similar frequenceis, that suggests a recent admixture imo.

I really hope they find the population that corresponds to them soon, that will be the greatest discovery in population genetics ever.

IronSide
06-02-18, 18:33
A nice map

https://upload.wikimedia.org/wikipedia/commons/8/80/MtDNA_haplogroup_tree_and_distribution_map.gif

bicicleur
06-02-18, 18:44
A nice map

https://upload.wikimedia.org/wikipedia/commons/8/80/MtDNA_haplogroup_tree_and_distribution_map.gif

what haplos are found in the light blue Central Asia?

bicicleur
06-02-18, 18:45
I wonder if Basal Eurasians left only their mtDNA as proof of their existence ... maybe they were a female dominated culture, it doesn't seem that the Basal in Iran Neolithic and Natufians were that much differentiated and they existed in similar frequenceis, that suggests a recent admixture imo.
I really hope they find the population that corresponds to them soon, that will be the greatest discovery in population genetics ever.

the Basal Eurasians are older than any Eurasian mtDNA haplogroup, but some of them must have gotten admixed with Basal Eurasian and others not

IronSide
06-02-18, 18:49
what haplos are found in the light blue Central Asia?

None were exclusively labeled to central Asia, I think its light blue to indicate commonality between East,South, and West Eurasia. The blue ones are West Eurasians

Angela
06-02-18, 19:14
We know Natufians were only partly Basal Eurasian. Hotu is the sample with the most Basal Eurasian. Natufians and Iran Neo were similar in terms of percentages.

It was in the Lazaridis paper:
https://www.nature.com/articles/nature19310

This is an open access version:
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5003663/pdf/nihms-804247.pdf

We discussed it in the thread here about the Melinda Yang paper, where we came to the conclusion that they just have a typo in there about which group has the most.
https://www.eupedia.com/forum/threads/35297-Insights-into-Modern-Human-Prehistory-Using-Ancient-Genomes?highlight=Basal+Eurasian

Ygorcs
06-02-18, 19:16
what haplos are found in the light blue Central Asia?

Really, is the Mt-DNA of East Siberians mostly West Eurasian? Or are they considering "Russians" as the entire country from the Baltic to the Pacific?

IronSide
06-02-18, 19:23
We know Natufians were only partly Basal Eurasian. If my memory serves, Hotu is the sample with the most Basal Eurasian. Natufians and Iran Neo were similar in terms of percentages.

Yes thats right, half of their ancestry is Basal and the other two is something related to WHG in the case of Natufians, and something descended from Ancient North Eurasians in the case of Iran Neo.

An important question to ask is who colonized the Near East first ? BEu or the other two groups ? we demand ancient dna from the paleolithic Near East !!!

IronSide
06-02-18, 19:33
Alright this is a daring hypothesis: N1,N2 and X are Basal Eurasian in origin, while H,V,J,T,U are WHG, UHG, and EHG in origin.

bicicleur is going to kill me :) sorry man but I can't accept that they left no mtDNA and Y-DNA but we only inherited their autosomal, I find that very unlikely.

bicicleur
06-02-18, 19:59
Alright this is a daring hypothesis: N1,N2 and X are Basal Eurasian in origin, while H,V,J,T,U are WHG, UHG, and EHG in origin.

bicicleur is going to kill me :) sorry man but I can't accept that they left no mtDNA and Y-DNA but we only inherited their autosomal, I find that very unlikely.

Basal Eurasians split from non-Africans earlier than 45 ka Usht-Ishim.
There are not so many options left.

bicicleur
06-02-18, 20:02
Yes thats right, half of their ancestry is Basal and the other two is something related to WHG in the case of Natufians, and something descended from Ancient North Eurasians in the case of Iran Neo.


that seems to be correct, but can you provide me the source where you got that info?

Angela
06-02-18, 20:09
that seems to be correct, but can you provide me the source where you got that info?

See post N. 7.

Jovialis posted this in the Melinda Yang thread:

Here's an excerpt from the original source:

https://i.imgur.com/ickCdsG.png

Angela
06-02-18, 20:22
Some more from Lazaridis:

"West Eurasians harbour significantly less Neanderthal ancestry than East Asians19-21, whichcould be explained if West Eurasians (but not East Asians) have partial ancestry from asource diluting their Neanderthal inheritance22. Supporting this theory, we observe anegative correlation between Basal Eurasian ancestry and the rate of shared alleles withNeanderthals19 (Supplementary Information, section 5; Fig. 2). By extrapolation, we inferthat the Basal Eurasian population had lower Neanderthal ancestry than non-Basal Eurasianpopulations and possibly none (ninety-five percent confidence interval truncated at zero of0-60%; Fig. 2; Methods). The finding of little if any Neanderthal ancestry in Basal Eurasianscould be explained if the Neanderthal admixture into modern humans 50,000-60,000 yearsago11 largely occurred after the splitting of the Basal Eurasians from other non-Africans.It is striking that the highest estimates of Basal Eurasian ancestry are from the Near East,given the hypothesis that it was there that most admixture between Neanderthals and modernhumans occurred19,23. This could be explained if Basal Eurasians thoroughly admixed intothe Near East before the time of the samples we analyzed but after the Neanderthaladmixture. Alternatively, the ancestors of Basal Eurasians may have always lived in the NearEast, but the lineage of which they were a part did not participate in the Neanderthaladmixture"

"A population without Neanderthal admixture, basal to other Eurasians, may have plausiblylived in Africa. Craniometric analyses have suggested an affinity between the Natufians andpopulations of north or sub-Saharan Africa24,25, a result that finds some support from Ychromosome analysis which shows that the Natufians and successor Levantine Neolithicpopulations carried haplogroup E, of likely ultimate African origin, which has not beendetected in other ancient males from West Eurasia (Supplementary Information, section6) 7,8. However, no affinity of Natufians to sub-Saharan Africans is evident in our genomewideanalysis, as present-day sub-Saharan Africans do not share more alleles with Natufiansthan with other ancient Eurasians (Extended Data Table 1). (We could not test for a link topresent-day North Africans, who owe most of their ancestry to back-migration fromEurasia26,27.) The idea of Natufians as a vector for the movement of Basal Eurasian ancestryinto the Near East is also not supported by our data, as the Basal Eurasian ancestry in theNatufians (44±8%) is consistent with stemming from the same population as that in theNeolithic and Mesolithic populations of Iran, and is not greater than in those populations(Supplementary Information, section 4). Further insight into the origins and legacy of theNatufians could come from comparison to Natufians from additional sites, and to ancientDNA from north Africa. "

This is why I started to consider perhaps a movement from India into Mesopotamia and then a spread from there.

IronSide
06-02-18, 20:24
that seems to be correct, but can you provide me the source where you got that info?
From Lazaridis et al (2016) https://www.biorxiv.org/content/early/2016/06/16/059311
Supplementary information page 34:

Neolithic Iran and Natufians could be derived from the same Basal Eurasian population but are genetically closer to EHG and WHG respectively. We take the model of Fig. S4.9 and attempt to fit Natufians as a mixture of the same Basal Eurasian population that contributes to Iran_N and any other population of the tree. Several solutions are feasible, and we show the best one (lowest ADMIXTUREGRAPH score) in Fig. S4.10. We can add both EHG and MA1 as simple branches to the model structure of Fig. S4.10 and show the results in Fig. S4.11. An interesting aspect of this model is that it derives both Natufians and Iran_N from Basal Eurasians but Natufians have ancestry from a population related to WHG, while Iran_N has ancestry related to EHG. Natufians and Iran_N may themselves reside on clines of WHG-related/EHG-related admixture. The fact that these two populations are differentially related to European hunter-gatherers can be directly seen from the following statistics:


X
Y
f4(Iran_N,Natufian;X,Y)
Z


EHG
Mbuti
0.00204
3.4


WHG
Mbuti
-0.00241
-4.3


WHG
EHG
-0.00441
-8.9


The statistic f4(Iran_N, Iran_HotuIIIb; EHG, Mbuti) = -0.00199 (Z=-2.4) suggests that the singleton individual from Hotu (Iran_HotuIIIb) was shifted towards EHG along the Iran_N/EHG cline, albeit it does not reach |Z|>3. There is uncertainty about the date of Iran_HotuIIIb, as it is not certain that it is of Mesolithic age and thus predates the Neolithic of Iran from Ganj Dareh. The fact that the Caucasus hunter-gatherers (CHG) (who are definitely pre-Neolithic) have extra EHG-related ancestry is also supportive of a substantial antiquity of this element in the Caucasus-Iran region. It is not clear whether the hunter-gatherers preceding the Neolithic in Ganj Dareh were similar to Iran_HotuIIIb or the CHG and their EHG affinity was diluted during Neolithization, or whether they are descended from an unsampled hunter-gatherer population that already had this reduced affinity to the EHG.

https://3.bp.blogspot.com/-voBU6e60Ox8/V-EUTr9ioUI/AAAAAAAAFY0/_l8r07RsZd4fg6ORn-WbI_mU8GeiZmQMQCLcB/s1600/14avas9.jpg

bicicleur
06-02-18, 22:15
Some more from Lazaridis:

"West Eurasians harbour significantly less Neanderthal ancestry than East Asians19-21, whichcould be explained if West Eurasians (but not East Asians) have partial ancestry from asource diluting their Neanderthal inheritance22. Supporting this theory, we observe anegative correlation between Basal Eurasian ancestry and the rate of shared alleles withNeanderthals19 (Supplementary Information, section 5; Fig. 2). By extrapolation, we inferthat the Basal Eurasian population had lower Neanderthal ancestry than non-Basal Eurasianpopulations and possibly none (ninety-five percent confidence interval truncated at zero of0-60%; Fig. 2; Methods). The finding of little if any Neanderthal ancestry in Basal Eurasianscould be explained if the Neanderthal admixture into modern humans 50,000-60,000 yearsago11 largely occurred after the splitting of the Basal Eurasians from other non-Africans.It is striking that the highest estimates of Basal Eurasian ancestry are from the Near East,given the hypothesis that it was there that most admixture between Neanderthals and modernhumans occurred19,23. This could be explained if Basal Eurasians thoroughly admixed intothe Near East before the time of the samples we analyzed but after the Neanderthaladmixture. Alternatively, the ancestors of Basal Eurasians may have always lived in the NearEast, but the lineage of which they were a part did not participate in the Neanderthaladmixture"

"A population without Neanderthal admixture, basal to other Eurasians, may have plausiblylived in Africa. Craniometric analyses have suggested an affinity between the Natufians andpopulations of north or sub-Saharan Africa24,25, a result that finds some support from Ychromosome analysis which shows that the Natufians and successor Levantine Neolithicpopulations carried haplogroup E, of likely ultimate African origin, which has not beendetected in other ancient males from West Eurasia (Supplementary Information, section6) 7,8. However, no affinity of Natufians to sub-Saharan Africans is evident in our genomewideanalysis, as present-day sub-Saharan Africans do not share more alleles with Natufiansthan with other ancient Eurasians (Extended Data Table 1). (We could not test for a link topresent-day North Africans, who owe most of their ancestry to back-migration fromEurasia26,27.) The idea of Natufians as a vector for the movement of Basal Eurasian ancestryinto the Near East is also not supported by our data, as the Basal Eurasian ancestry in theNatufians (44±8%) is consistent with stemming from the same population as that in theNeolithic and Mesolithic populations of Iran, and is not greater than in those populations(Supplementary Information, section 4). Further insight into the origins and legacy of theNatufians could come from comparison to Natufians from additional sites, and to ancientDNA from north Africa. "

This is why I started to consider perhaps a movement from India into Mesopotamia and then a spread from there.

I think there is discontinuity between pre-LGM and post-LGM SW Asia.
During LGM populations from the Nile delta (E), the Indusdelta/India (H2, G + Basal Eurasian admixture) and Transcaucasia (J) mixed there.
It would explain a lot, but not the observed ancestry between Iran neo and EHG at one hand and between Natufian and WHG on the other hand.

Angela
06-02-18, 23:24
I think there is discontinuity between pre-LGM and post-LGM SW Asia.
During LGM populations from the Nile delta (E), the Indusdelta/India (H2, G + Basal Eurasian admixture) and Transcaucasia (J) mixed there.
It would explain a lot, but not the observed ancestry between Iran neo and EHG at one hand and between Natufian and WHG on the other hand.

Couldn't movement back and forth across the Caucasus, or perhaps further east explain the admixture in the Northern Near East?

We now have two J1 in the far northeast who don't seem to have any Basal Eurasian, yes?

halfalp
07-02-18, 00:15
I dont understand how between Vindija, Mezmeskaya and Altai, the third have given none ancestry to modern humans, how East Asian can be more Neanderthal than West Eurasians. Are they put Homo Denisova in the same level as Neanderthal, or are Oase related people, really some ancestors of East Asians ? It's all very weird, apparently the neanderthal input in sapiens is near Vindija and Mezmeskaya, a little more from the latter, so are we talking about a ghost neanderthal population for heritage in sapiens ? Maybe some unidentified Siberian Neanderthals, dont know...

IronSide
07-02-18, 01:43
Couldn't movement back and forth across the Caucasus, or perhaps further east explain the admixture in the Northern Near East?

We now have two J1 in the far northeast who don't seem to have any Basal Eurasian, yes?

Haplogroups J and R appeared both in Neolithic Iran and Caucasus, and north in the Steppe and Baltic, and EHG is the shared ancestry between them, J1 didn't seem to have Basal, so is it blasphemous to say that haplogroup J is actually EHG that moved south ?

Angela
07-02-18, 02:09
Haplogroups J and R appeared both in Neolithic Iran and Caucasus, and north in the Steppe and Baltic, and EHG is the shared ancestry between them, J1 didn't seem to have Basal, so is it blasphemous to say that haplogroup J is actually EHG that moved south ?

I've been thinking about that too, whether IJ might have split north of the Caucasus somewhere. That, or those "I" lines went north before Basal Eurasian showed up, or the BE just got diluted to nothing through successive mating.

I haven't checked dates of those clades or anything like that; just idle musing.

Bicicleur might have a better handle on it.

bicicleur
07-02-18, 08:33
I've been thinking about that too, whether IJ might have split north of the Caucasus somewhere. That, or those "I" lines went north before Basal Eurasian showed up, or the BE just got diluted to nothing through successive mating.

I haven't checked dates of those clades or anything like that; just idle musing.

Bicicleur might have a better handle on it.

my guess is that IJ split 42.9 ka in Transcaucasia
and J stayed in Georgia, Dzudzuana and Ortvale Klde caves
while I entered Europe via Mezmayskaya 39 ka

Some I would have mixed 35 ka with the Kostenki population, which gave way to the Vestonice cluster,
others would not have mixed :
- the El Miron cluster mixed later in western Europe with Goyet 35 ka like
- the Villabruna cluster stayed pretty unmixed till they meat some people from Anatolia some 15 ka

There is also C1a2 in mesolithic Anatolia.
They may be descendants of the Vestonice cluster moving south during LGM.

bicicleur
07-02-18, 08:47
Haplogroups J and R appeared both in Neolithic Iran and Caucasus, and north in the Steppe and Baltic, and EHG is the shared ancestry between them, J1 didn't seem to have Basal, so is it blasphemous to say that haplogroup J is actually EHG that moved south ?
I guess those J in Karelia split from the main branch of J in Transcaucasia pretty early, some 15 ka.
J in Transcaucasia must have received Basal Eurasian a little later.
I guess they received it from incoming G from the Zagros Mountains.
GxG2a2 was observed in neolithic Zagros, we don't have mesolithic Zagros.
G might have survived LGM in the dry bed of the Persian Gulf.
G2a2 moved northwest into obsidian-rich Cappadocia as early as 17 ka, when it split further into G2a2a and G2a2b.
As early as 16 ka obsidian from Cappadocia arrived in the Upper Eurphrate and the Levant, just south of Lebanon.
But I think already before, the Natufians had received Basal Eurasian from incoming H2.
Natufian E1b1b1 originaly didn't have Basal Eurasian, they were African, Mota 4.5 ka like.

IronSide
07-02-18, 12:48
@bicicleur

but autosomally Natufians didn't have African. or did they ?

bicicleur
07-02-18, 16:51
@bicicleur
but autosomally Natufians didn't have African. or did they ?

I don't know
and then there is North African and SSA

didn't the 7 ka northern Morroccan DNA share DNA with Natufians? they were half Natufian and half western Africa?

Angela
07-02-18, 23:37
I don't know
and then there is North African and SSA

didn't the 7 ka northern Morroccan DNA share DNA with Natufians? they were half Natufian and half western Africa?

I think we posted the provisional answer upthread from Lazaridis in "The Genetic Structure of the World's First Farmers":

"However, no190 affinity of Natufians to sub-Saharan Africans is evident in our genome-wide analysis, as191 present-day sub-Saharan Africans do not share more alleles with Natufians than with other192 ancient Eurasians (Extended Data Table 1). (We could not test for a link to present-day NorthAfricans, who owe most of their ancestry to back-migration from Eurasia27,28 193 .)"

https://www.biorxiv.org/content/biorxiv/early/2016/06/16/059311.full.pdf

IronSide
08-02-18, 06:54
I think we posted the provisional answer upthread from Lazaridis in "The Genetic Structure of the World's First Farmers":

"However, no190 affinity of Natufians to sub-Saharan Africans is evident in our genome-wide analysis, as191 present-day sub-Saharan Africans do not share more alleles with Natufians than with other192 ancient Eurasians (Extended Data Table 1). (We could not test for a link to present-day NorthAfricans, who owe most of their ancestry to back-migration from Eurasia27,28 193 .)"

https://www.biorxiv.org/content/biorxiv/early/2016/06/16/059311.full.pdf

Yes, they didn't have sub-Saharan admixture. I don't know why some Gedmatch calculators return results like this one Gedrosia K3

kit M041601 (Natufian)



Population



E_Eurasian
-


SSA
10.80


W_Eurasian
89.20



Well, Natufians did have higher basal than modern Middle Easterners, so the excess of that was assigned to SSA ? or that all of them are just terrible.

Promenade
08-02-18, 07:26
Could SSA showing up in Natufians have something to do with Natufian Ancestry in East Africa? Luxmanda derived well over a third of her ancestry from the Neolithic Levant with no CHG or EEF contribution.

It's suggested that either there was a migration from the Levant to east Africa or that Luxmanda and PPN-Levantine farmers shared a common ancestor. Hunter Gatherers from Ethiopia just 1,400 years before Luxmanda lack any west Eurasian ancestry which points to a migration, but a pure stream of Natufian ancestry entering east Africa some time after 2,500bc needs some explaining.

Angela
08-02-18, 18:12
Yes, they didn't have sub-Saharan admixture. I don't know why some Gedmatch calculators return results like this one Gedrosia K3

kit M041601 (Natufian)



Population



E_Eurasian
-


SSA
10.80


W_Eurasian
89.20



Well, Natufians did have higher basal than modern Middle Easterners, so the excess of that was assigned to SSA ? or that all of them are just terrible.

I think I might go with door number 2. :) It's just never going to be that accurate to use programs based on modern populations to analyze ancient ones. It may give you a rough idea, but small percents of one thing or another may be off.

Seriously, as I pointed out above, in the original analyses of the SHG they came out with a chunk of African.