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Angela
23-01-19, 18:01
See:

G.Gonzalez-Fortes et al:
https://royalsocietypublishing.org/doi/full/10.1098/rspb.2018.2288

"Being at the western fringe of Europe, Iberia had a peculiar prehistory and a complex pattern of Neolithization. A few studies, all based on modern populations, reported the presence of DNA of likely African origin in this region, generally concluding it was the result of recent gene flow, probably during the Islamic period. Here, we provide evidence of much older gene flow from Africa to Iberia by sequencing whole genomes from four human remains from northern Portugal and southern Spain dated around 4000 years BP (from the Middle Neolithic to the Bronze Age). We found one of them to carry an unequivocal sub-Saharan mitogenome of most probably West or West-Central African origin, to our knowledge never reported before in prehistoric remains outside Africa. Our analyses of ancient nuclear genomes show small but significant levels of sub-Saharan African affinity in several ancient Iberian samples, which indicates that what we detected was not an occasional individual phenomenon, but an admixture event recognizable at the population level. We interpret this result as evidence of an early migration process from Africa into the Iberian Peninsula through a western route, possibly across the Strait of Gibraltar."

If correct, it means that once again the programs purporting to date admixture seem to pick up only the most recent event.

Jovialis
23-01-19, 18:26
Very interesting

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

berun
23-01-19, 19:05
yes, very interesting, now as the steppe autosomal in COV20126 is linked to African mt DNA I must admit that the steppe theory is right... only to change the Pontic steppe by the Sahel one!
;)

just irony, realy I need much to deal with Reich fans

Angela
23-01-19, 19:22
yes, very interesting, now as the steppe autosomal in COV20126 is linked to African mt DNA I must admit that the steppe theory is right... only to change the Pontic steppe by the Sahel one!
;)

just irony, realy I need much to deal with Reich fans

There is no "steppe" in that sample: it's typical Iberian Middle Neolithic/Chalcolithic.

Plus, since you like irony: what a surprise if mtDna and yDna in a sample should come from different migrations from different time periods. That would overturn all modern population genetics! :)

berun
23-01-19, 19:36
quite weird, at K7 neither steppe nor BB / CWC display CHG

berun
23-01-19, 19:44
Alain Affelou:

The WHG (orange) and Anatolian Neolithic (blue) are the major genome components in all our four Iberian samples, although at K = 7, a component (pink) associated with the Russian Steppes, is already visible in COV20126.

ToBeOrNotToBe
23-01-19, 21:23
quite weird, at K7 neither steppe nor BB / CWC display CHG

What do you mean, I swear BB has CHG, and CWC definitely has quite a lot of it. Is that what this paper says?

Angela
23-01-19, 21:34
None at K6, at K7 the tiniest smidgeon of "steppe".

All as expected I would say...a late, gradual entrance into Iberia.

It doesn't matter whether it's a big lab or a small one, international/American, or Spanish. The narrative is consistent.

berun
23-01-19, 21:55
What do you mean, I swear BB has CHG, and CWC definitely has quite a lot of it. Is that what this paper says?
at K6 the green CHG is present in steppe and CWC, at K7 the green which is 2/3 in CHG disappears in such pops, weird, but to me ok as it goes for my first bet about IE from Kievan Rus.

bicicleur
24-01-19, 12:39
at K6 the green CHG is present in steppe and CWC, at K7 the green which is 2/3 in CHG disappears in such pops, weird, but to me ok as it goes for my first bet about IE from Kievan Rus.

very weird
at K=7 the CHG splits in 2 components, and only one of them is in steppe

I guess this is one of the flaws of K admixture, which splits into different components depending on what populations are compared in the mix

bicicleur
24-01-19, 13:42
None at K6, at K7 the tiniest smidgeon of "steppe".

All as expected I would say...a late, gradual entrance into Iberia.

It doesn't matter whether it's a big lab or a small one, international/American, or Spanish. The narrative is consistent.

at K7 there is a diluted but clear signal of steppe in BA Iberia which wasn't there in MN/Chl Iberia
it has to do with the R1b-P312 expansion in Europe, which was not accompanied by any specific mtDNA : they took local wives along the way of their expansion

berun
24-01-19, 16:08
if you accept K7 then you must accept that Iran Neolithic and Anatolia Chalco had already been invaded by Yamnayans before they popped up in the steppes... weird again?

halfalp
24-01-19, 18:19
yes, very interesting, now as the steppe autosomal in COV20126 is linked to African mt DNA I must admit that the steppe theory is right... only to change the Pontic steppe by the Sahel one!
;)

just irony, realy I need much to deal with Reich fans

See just like i said in another thread, you are quoting Steppe or IE's without even being it the matter of the subject...

halfalp
24-01-19, 18:26
I must be blind but where exactly this sentence " Our analyses of ancient nuclear genomes show small but significant levels of sub-Saharan African affinity in several ancient Iberian samples, which indicates that what we detected was not an occasional individual phenomenon, but an admixture event recognizable at the population level. " Is shown into the admixture chart?

bicicleur
24-01-19, 20:05
I must be blind but where exactly this sentence " Our analyses of ancient nuclear genomes show small but significant levels of sub-Saharan African affinity in several ancient Iberian samples, which indicates that what we detected was not an occasional individual phenomenon, but an admixture event recognizable at the population level. " Is shown into the admixture chart?

it's not in the PCA, nor in K6 or K7
it is only detectable with D- and f3-statistics

berun
24-01-19, 20:19
Even as they dont find SSA admixture in the individual with African mtDNA they downgrade other samples till get such admixture... but the guy is so problematic that he dont display it even so.
:)

For these programs I'm getting the impression that behave like the best Marx bro.

10645

halfalp
24-01-19, 20:22
it's not in the PCA, nor in K6 or K7
it is only detectable with D- and f3-statistics

And do we know what kind of sub-saharian ancestry did they found, what was the prehistoric proxy for it Mota, Nachikufu? Or is it modern SSA ancestry? Also why they express specifically an emphasis on SSA ancestry and not African one in general? Hard time to imagine that individual in prehistoric Spain with SSA ancestry, didn't have North African ancestry too no?

Megalophias
24-01-19, 21:54
SSA proxies were ancient South Africans: Ballito Bay (Khoisan) and Iron Age (Bantu), both gave (barely) significant D stats.

bicicleur
24-01-19, 22:03
SSA proxies were ancient South Africans: Ballito Bay (Khoisan) and Iron Age (Bantu), both gave (barely) significant D stats.

how old is the Ballito Bay (Khoisan)?
were they herders or HG?

domesticated animals arrived in S.-Africa ca 2 ka through contact with herders from PPNB Levantine descent

Mota or the Malawi HG would have been a better reference to compare against

bicicleur
24-01-19, 22:13
according to Ted Kendal, this is the Y-DNA :
Ted Kandell is met Max De Plum en 3 anderen.
19 januari om 21:23
The new Ancient Iberian Genomes unpublished study, PRJEB29189, has three whole genomes that have high-coverage Y-DNA sequences from 4500-3500 ybp. Vadim, can you add these to the YFull tree?
No "Steppe" / "Bell Beaker" ancestry in Iberia yet.
The haplogroups are as follows.
Who are the "lucky winners" here who match them on the YFull tree?
A spreadsheet of all the Y SNPs for these ancient Iberian individuals:
https://docs.google.com/…/1thcQUVLKga7YPtv1mj0d9fakXD…/edit…
https://www.ebi.ac.uk/ena/data/view/PRJEB29189
LU339 "partial" I-Y3749:
https://yfull.com/tree/I-Y3749/
AMM080/Y4661/FGC7133+
FGC7139/Y3749-
COV20126 I-Y34539*:
https://yfull.com/tree/I-Y34539/
LD270 "partial" H-Y20838:
https://yfull.com/tree/H-Y20838/
Z19077+
Z19083+
Z19118+
Y21665-
Y21636-
Y20840-
Y20836-
Y21673-
Y21633-
Y21635-
Y21640-

it doesn't match the Y-DNA published in the study itself (G2a2b)
a sloppy job?

halfalp
24-01-19, 22:21
how old is the Ballito Bay (Khoisan)?
were they herders or HG?

domesticated animals arrived in S.-Africa ca 2 ka through contact with herders from PPNB Levantine descent

Mota or the Malawi HG would have been a better reference to compare against

Yes the Malawi HG is Nachikufu.

halfalp
24-01-19, 22:35
But there is something i dont really understand " An alternative possibility is that gene flow may have occurred even earlier in Southern Iberia from a population with Sub-Saharan African features, which left some genetic contribution in the genomes of the people, the local hunter–gatherers, they admixed with " I'm not sure how prehistoric Iberians and prehistoric Sub-Saharian Africans are supposed to have mixed without Iberomaurusian-related ancestry being more dominant than the Sub-Saharian One. Also the mtdna L2a1 shows no SSA ancestry at all, wich could mean that the lineage was at the time enough old in that place to have her SSA ancestry diluted into Neolithic ones. It's then possible that the SSA ancestry was related with a North African ancestry older than Iberomaurusians and more close to SSA, less Basal Eurasian.

Megalophias
24-01-19, 23:20
Yeah, it's weird. L2a1 and L1b are clear enough indicators, but the D stat signal is pretty marginal, should we be sure it's even real? Seems like it wouldn't take much of undetected artifact somewhere to throw them off.

In general f stats involving Africans are hard to interpret, and I'll be surprised if the real population history isn't way more complicated than any qpGraph yet attempted.

bicicleur
25-01-19, 00:09
But there is something i dont really understand " An alternative possibility is that gene flow may have occurred even earlier in Southern Iberia from a population with Sub-Saharan African features, which left some genetic contribution in the genomes of the people, the local hunter–gatherers, they admixed with " I'm not sure how prehistoric Iberians and prehistoric Sub-Saharian Africans are supposed to have mixed without Iberomaurusian-related ancestry being more dominant than the Sub-Saharian One. Also the mtdna L2a1 shows no SSA ancestry at all, wich could mean that the lineage was at the time enough old in that place to have her SSA ancestry diluted into Neolithic ones. It's then possible that the SSA ancestry was related with a North African ancestry older than Iberomaurusians and more close to SSA, less Basal Eurasian.

I've been wondering that too.
Prior to Iberomaurisian there was Aterian, which descended from the archaic Jebel Irhoud population (315 ka), so not the SSA.
If SSA entered Iberia, these people must have crossed Iberomaurisian territory prior to that.

Corrado
25-01-19, 02:02
Yeah, it's weird. L2a1 and L1b are clear enough indicators, but the D stat signal is pretty marginal, should we be sure it's even real? Seems like it wouldn't take much of undetected artifact somewhere to throw them off.

In general f stats involving Africans are hard to interpret, and I'll be surprised if the real population history isn't way more complicated than any qpGraph yet attempted.


Hard to interpret in what way?

Megalophias
25-01-19, 04:36
In that you could probably get the same results from a variety of histories involving who knows what mixtures and ghost populations; and on top of that there's reference bias and perhaps other artifacts to consider.

Corrado
25-01-19, 05:05
In that you could probably get the same results from a variety of histories involving who knows what mixtures and ghost populations

Are you implying false postitive results, as in a population showing a signature of African admixture in f statistics but it's maybe not indicative of straightforward African ancestry? Couldn't you have this potentiality with any population, not just Africans?



and on top of that there's reference bias and perhaps other artifacts to consider.

Can you elaborate a bit more? I take it you have some personal experience using these software packages.

Megalophias
25-01-19, 18:36
No, I don't do any of this stuff, just looking at other people's results. Yes, marginal results could be misleading in any case. Africa is only worse because there is such deep diverse branching mixed together and much less ancient DNA.

MOESAN
25-01-19, 20:23
very weird
at K=7 the CHG splits in 2 components, and only one of them is in steppe

I guess this is one of the flaws of K admixture, which splits into different components depending on what populations are compared in the mix

It's what I find unpleasant since some studies: inconsistance of admixtures runs from survey to survey. Impossibility to compare quietly. Aside IBD what is of worth?

berun
25-01-19, 20:37
it's worth to know that if someone tries hard, it can be founf SSA admixture, or Mongolian steppe admixture, no matter.

halfalp
25-01-19, 21:03
I've been wondering that too.
Prior to Iberomaurisian there was Aterian, which descended from the archaic Jebel Irhoud population (315 ka), so not the SSA.
If SSA entered Iberia, these people must have crossed Iberomaurisian territory prior to that.

We dont have Iberomaurusian samples from all their existence, only from Epipaleolithic. It's very possible that, early Iberomaurusians were genetically different than later ones. Just like Gravettians were C1a2 people that were replaced with R1b in Epigravettian with a different ancestry cf. ( dolni vestonice against villabruna cluser ). But at the same level, it's frustrating to know that a place lile Iberia who is the dominant place in Europe for prehistoric Archeology, cannot give us more samples than Eastern Europe.

Jack Johnson
03-02-19, 03:09
We so far have mtDNA haplogroups L2a1 and L1b1a in Neolithic/Chalcolithic Iberia, and a L2a1 sample from the Pre-Pottery Neolithic culture located in Tell Halula, Syria. These samples do not have any Sub-Saharan African admixture correct? If I recall in the Lazaridis et al. 2018 preprint, the Iberomaurusians were demonstrated to have had no SSA ancestry, and they contributed ancestry to Sub-Saharan Africans not the other way around. It could be that the Iberomaurusians and/or their descendants contributed ancestry to some of the peoples of Neolithic Western and Southern Europe. That may explain why mtDNA Haplogroups L2a1 and L1b1a show up in Neolithic/Copper Age Iberia. Seeing that mtDNA haplogroups L2 and L1 both predate the widely accepted date of Homo Sapiens entry into Eurasia at 70,000 ybp, is it possible that like Y-DNA haplogroups A, B, BT, and CT, various subclades of mtDNA haplogroup L were part of the original gene pool of the first Eurasians?

halfalp
03-02-19, 15:22
We so far have mtDNA haplogroups L2a1 and L1b1a in Neolithic/Chalcolithic Iberia, and a L2a1 sample from the Pre-Pottery Neolithic culture located in Tell Halula, Syria. These samples do not have any Sub-Saharan African admixture correct? If I recall in the Lazaridis et al. 2018 preprint, the Iberomaurusians were demonstrated to have had no SSA ancestry, and they contributed ancestry to Sub-Saharan Africans not the other way around. It could be that the Iberomaurusians and/or their descendants contributed ancestry to some of the peoples of Neolithic Western and Southern Europe. That may explain why mtDNA Haplogroups L2a1 and L1b1a show up in Neolithic/Copper Age Iberia. Seeing that mtDNA haplogroups L2 and L1 both predate the widely accepted date of Homo Sapiens entry into Eurasia at 70,000 ybp, is it possible that like Y-DNA haplogroups A, B, BT, and CT, various subclades of mtDNA haplogroup L were part of the original gene pool of the first Eurasians?

BT and CT were already found in some Paleolithic Europeans and Neolithic Middle-Easterns, but i dont know if they lacked SNP's, so actually the BT and CT individuals might more likely be just C1a2 or C1b. As for Iberomaurusians, it's a little bit complicated because Iberomaurusians and Natufians have a clear shared ancestry, and the mtdna U6 in Iberomaurusians, is probably not native North African. As i said in my post, it would be interesting to have early Iberomaurusian samples, instead of the late one that we have. The genetic signatures might been different in the two groups. It's like comparing Gravettians of the Vestonice Cluster and Epi-Gravettians of the Villabruna Cluster. As far as the mtdna L samples, at this point it's hard to have any conclusions because this L2a1 individual from Iberia have no SSA ancestry, but doesn't have Iberomaurusian ancestry either. It might just mean that her ancestors were already here to take in the face the Neolithic ancestry and lose entirely their previous ancestry, or something like that.

MOESAN
03-02-19, 21:04
I've been wondering that too.
Prior to Iberomaurisian there was Aterian, which descended from the archaic Jebel Irhoud population (315 ka), so not the SSA.
If SSA entered Iberia, these people must have crossed Iberomaurisian territory prior to that.

Ancient physical anthropology spoke of the 'grimaldi' type in mediterranea, modified over time and almost disappearing in late Neolithic; showing the most of its features very close to 'cro-magnon' but with some features evocating 'negroid' (old namings). A fragrence of AFN old cultures? mixture or old badly differentiated types, as what occurred in South SIberia?

Jack Johnson
07-02-19, 07:47
Thanks for your input. I always thought that—along with Y-dna A and C—mtdna L was a surviving lineage of the original Eurasians. That’s why mtdna L and Y-dna A are found in Northern Europe and parts of West Asia. Is there an ancient mtdna database online by chance? I am still trying to find a link to that L2a1 Tell Halula sample.

halfalp
08-02-19, 10:52
Thanks for your input. I always thought that—along with Y-dna A and C—mtdna L was a surviving lineage of the original Eurasians. That’s why mtdna L and Y-dna A are found in Northern Europe and parts of West Asia. Is there an ancient mtdna database online by chance? I am still trying to find a link to that L2a1 Tell Halula sample.

mtdna L and y-dna A must been recent commers to Northern Europe, they never were found in Paleolithic and Neolithic samples to date. There was a minor hypothesis that y-dna E and mtdna L3 were in fact Eurasian coming back to Africa, but it's hard to conciliate with the datas, y-dna E was found in the Levantine Natufians but not mtdna L3 ( or any other L ). I didn't know about the Tell Halula sample until you spoked of it, and i cannot found anything in the prehistoric samples interactive map i used in general. There was a website from Jean Manco wich repertoriate an amazing set of samples from almost every studies on ancient dna, but unfortunately she past out and the website eventually shut down. But even, i dont recall have found an L2 from Tell Halula in her tables.

The only prehistoric mtdna L samples i know are:

Mota 1, Ethiopia, 2'500 BC: Y-dna E1b1, Mtdna L3X2a.

Pastoral Neolithic, Tanzania, 1200-940 BC: mtdna L2a1.

Malawi Stone Age, Malawi, 700-400 BC: mtdna L0f.

Nachikufu, Malawi, 8000-3000 BC: Y-dna BT, Mtdna L0K2.

And a few prehistoric HG's from South Africa, all y-dna A and mtdna L, probably ancestors of Khoikhoi people.

Also one of the Guanche sample from the Canaria Islands was: Mtdna L3b1a.

MOESAN
08-02-19, 23:17
it's worth to know that if someone tries hard, it can be founf SSA admixture, or Mongolian steppe admixture, no matter.

Short post. What will you mean here?
All the way, I'm not sure we know always separate little traces of admixture from very remote common heritage. I suppose it depends on length of shared segments?

Ygorcs
09-02-19, 01:19
Very interesting

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

How weird these admixture charts. Where is all the green of CHG or Iran Neolithic in the LNBA steppe? They show some Anatolian blue, Levantine puple even, but almost no green CHG. How is that so?

Ygorcs
09-02-19, 01:28
it's not in the PCA, nor in K6 or K7
it is only detectable with D- and f3-statistics

Then how can they define that as small but significant Subsaharan ancestry. Significant? It looks like some tiny residual ancestry picked up by Neolithic North Africans possibly related to the Cardial Ware in the southern Mediterranean coast, which also extended to/from Iberia. But I fail to see anything significant about those results. It happened, but apparently without major or even minor but notable impact.

Ygorcs
09-02-19, 06:38
We so far have mtDNA haplogroups L2a1 and L1b1a in Neolithic/Chalcolithic Iberia, and a L2a1 sample from the Pre-Pottery Neolithic culture located in Tell Halula, Syria. These samples do not have any Sub-Saharan African admixture correct? If I recall in the Lazaridis et al. 2018 preprint, the Iberomaurusians were demonstrated to have had no SSA ancestry, and they contributed ancestry to Sub-Saharan Africans not the other way around. It could be that the Iberomaurusians and/or their descendants contributed ancestry to some of the peoples of Neolithic Western and Southern Europe. That may explain why mtDNA Haplogroups L2a1 and L1b1a show up in Neolithic/Copper Age Iberia. Seeing that mtDNA haplogroups L2 and L1 both predate the widely accepted date of Homo Sapiens entry into Eurasia at 70,000 ybp, is it possible that like Y-DNA haplogroups A, B, BT, and CT, various subclades of mtDNA haplogroup L were part of the original gene pool of the first Eurasians?

1/3 of the ancestry of UP Iberomaurusians had close affinities to Subsaharan Africans, mainly a Hadza-like population, but it is indeed not found in any modern African population. My guess is that that 1/3 Hadza-like admixture represents the genetic structure of North Africa before West Eurasian back-migration that brought Basal Eurasian ancestry and other Eurasian admixtures that would eventually cause the high genetic affinity with the Natufians (who also had some North African input).

bicicleur
09-02-19, 10:37
1/3 of the ancestry of UP Iberomaurusians had close affinities to Subsaharan Africans, mainly a Hadza-like population, but it is indeed not found in any modern African population. My guess is that that 1/3 Hadza-like admixture represents the genetic structure of North Africa before West Eurasian back-migration that brought Basal Eurasian ancestry and other Eurasian admixtures that would eventually cause the high genetic affinity with the Natufians (who also had some North African input).

In the Dzudzuana study, it says that it is the other way around. There is no Yoruba in Iberomaurisians, there is Iberomaurisian in Yoruba.
So, no SSA in Iberomaurisian.

berun
09-02-19, 10:57
Short post. What will you mean here?
All the way, I'm not sure we know always separate little traces of admixture from very remote common heritage. I suppose it depends on length of shared segments?

the paper tries to state SSA ancestry in ancient Iberians when in admixture graphs they can't get even a trace, even among ancient Maghribins! so they go to downgrade other samples as to level them with the sample with mtDNA L till geting some SSA signal... but even so the sample with L is not prividing SSA (!!). this paper is like one demonstrating that Earth is flat providing photos from Australia, Italy and Canada showing a flat horizon.

MOESAN
10-02-19, 12:12
How weird these admixture charts. Where is all the green of CHG or Iran Neolithic in the LNBA steppe? They show some Anatolian blue, Levantine puple even, but almost no green CHG. How is that so?

??
It seems they made a 'steppe' component with the most of HG and CHG/Iran, putting the remnant of CHG/Iran in the Anatolian component???

halfalp
10-02-19, 12:31
Yeah those colors are weird, first why put Iran_N and Chl together, with that high of Anatolian ancestry, when they always told us that Iranian Farmers were distinct from Anatolians and Levantines ones. It's just confusing more. Also the Anatolian ancestry in SHG and the Iranian one in EHG is weird, it cannot be clear what is it about.

Can'tFightTruthM8s
10-02-19, 13:35
the paper tries to state SSA ancestry in ancient Iberians when in admixture graphs they can't get even a trace, even among ancient Maghribins! so they go to downgrade other samples as to level them with the sample with mtDNA L till geting some SSA signal... but even so the sample with L is not prividing SSA (!!). this paper is like one demonstrating that Earth is flat providing photos from Australia, Italy and Canada showing a flat horizon.

That analogy was beautiful.