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Fire Haired14
08-09-15, 04:57
http://cdn.phys.org/newman/csz/news/800/2015/2-ancientgenom.jpg
Source (http://phys.org/news/2015-09-ancient-genomes-link-early-farmers.html): "Illustration of every day life in the El Portalon cave during the Neolithic and Copper Age"


The Official name of the Paper is: Günther et al. (2015) Ancient genomes link early farmers from Atapuerca in Spain to modern-day Basques, PNAS.

It has not been published yet but will be soon here (http://www.pnas.org/content/early/recent) at PNAS. Here's a list of articles discussing the upcoming paper: Article#1 (http://www.bbc.co.uk/news/science-environment-34175224), Article# (http://phys.org/news/2015-09-ancient-genomes-link-early-farmers.html)2, Article#2 (http://www.uu.se/en/media/press-releases/press-release/?id=2816&area=3,8&typ=pm&lang=en), Article#3 (http://www.agenciasinc.es/Noticias/Los-vascos-proceden-de-los-primeros-agricultores-de-la-Peninsula).

Summary of information given by the Articles: 8 genomes ranging 5,500-3,500 years old from the El Portalón in Northern Spain were sampled. Of modern day Iberians they most closely resemble Basque. Other Iberians have ancestry from outside of Iberia that Basque lack(IMO, not completely). The El Portalón individuals had Lighter skin and darker eyes than Mesolithic Europeans and were lactose intolerant.

EDIT: Nature article with new Info LINK (http://news.sciencemag.org/archaeology/2015/09/unusual-relic-language-comes-small-group-farmers-isolated-thousands-years): It says non-Basque Iberians have 10-25% ancestry from new people who arrived in Iberia after the Neolithic and Basque and El Portalon genomes have 0%.

Of Ancient genomes Basque are closest to El Portalon. What this may mean is they're direct ancestors/close relatives of Basque not just generic EEF.

Also, 4/8 of the El Portalon genomes are Male. This means we'll get Y DNA. I hope we get Y DNA ranging each era. If R1b-L11 pops up with no ANE that'll debunk a Steppe origin for that lineage, if it doesn't and there's no ANE, that'll support a Steppe origin of R1b-L11.

Also from another Article LINK (http://sciencenordic.com/genetics-confirm-migrants-brought-farming-mediterranean): Quote from one of the authors: It doesn't make sense because Basque have ANE ancestry, the could not have been isolated for 5,000 years.

“Even though they clearly share common ancestry with early European farmers, we can see now that they have been rather isolated, genetically speaking, for at least the last 5,000 years,” says Jakobsson.

Brennos
08-09-15, 07:57
http://cdn.phys.org/newman/csz/news/800/2015/2-ancientgenom.jpg
Source (http://phys.org/news/2015-09-ancient-genomes-link-early-farmers.html): "Illustration of every day life in the El Portalon cave during the Neolithic and Copper Age"


The Official name of the Paper is: Günther et al. (2015) Ancient genomes link early farmers from Atapuerca in Spain to modern-day Basques, PNAS.

It has not been published yet but will be soon here (http://www.pnas.org/content/early/recent) at PNAS. Here's a list of articles discussing the upcoming paper: Article#1 (http://www.bbc.co.uk/news/science-environment-34175224), Article# (http://phys.org/news/2015-09-ancient-genomes-link-early-farmers.html)2, Article#2 (http://www.uu.se/en/media/press-releases/press-release/?id=2816&area=3,8&typ=pm&lang=en), Article#3 (http://www.agenciasinc.es/Noticias/Los-vascos-proceden-de-los-primeros-agricultores-de-la-Peninsula).

Summary of information given by the Articles: 8 genomes ranging 5,500-3,500 years old from the El Portalón in Northern Spain were sampled. Of modern day Iberians they most closely resemble Basque. Other Iberians have ancestry from outside of Iberia that Basque lack(IMO, not completely). The El Portalón individuals had Lighter skin and darker eyes than Mesolithic Europeans and were lactose intolerant.

EDIT: Nature article with new Info LINK (http://news.sciencemag.org/archaeology/2015/09/unusual-relic-language-comes-small-group-farmers-isolated-thousands-years): It says non-Basque Iberians have 10-25% ancestry from new people who arrived in Iberia after the Neolithic and Basque and El Portalon genomes have 0%.

Of Ancient genomes Basque are closest to El Portalon. What this may mean is they're direct ancestors/close relatives of Basque not just generic EEF.

Also, 4/8 of the El Portalon genomes are Male. This means we'll get Y DNA. I hope we get Y DNA ranging each era. If R1b-L11 pops up with no ANE that'll debunk a Steppe origin for that lineage, if it doesn't and there's no ANE, that'll support a Steppe origin of R1b-L11.

Also from another Article LINK (http://sciencenordic.com/genetics-confirm-migrants-brought-farming-mediterranean): Quote from one of the authors: It doesn't make sense because Basque have ANE ancestry, the could not have been isolated for 5,000 years.

We finally are at the door of truth about R1b history: I read your links and I underline this: all the articles point to an early migration of farmers from the East, so Y-DNA could be G2a or I2a. But, if they linked atapuerca with Basques, then I'd be prone to think they found some R1b-M269.

And also, I quote the last link, "We’ve seen in both Scandinavia and throughout central Europe that migration of people from the Fertile Crescent in the Near East brought farming techniques to Europe,” says Mattias Jakobsson, professor of genetics at Uppsala University, Sweden, and co-author of one of the new studies.“Now we can finally say the same for Iberia,” he says, talking about the new research, which has just been published today in the scientific journal PNAS (http://www.pnas.org/cgi/doi/10.1073/pnas.1509851112)." and the title itself, "Scientists have sequenced the genomes of early farmers from Spain, confirming that they descended from the same group of migrants who brought farming to Northern Europe."... so they are I2a like Motala?

gyms
08-09-15, 08:35
...so they are I2a like Motala?

No.Motala I2a is Mesolithic and not M26.

bicicleur
08-09-15, 08:48
interesting

I wonder what is the ratio G2a/I2a
maybe it will give insight in the expansion of I2a1a-M26

3500 yo R1b may be present, more than 5000 yo R1b-M269 would be a surprise

the fact that todays Baks are similar to neolithic Basks suggests the later R1b arrivals were males without wives

Maciamo
08-09-15, 09:33
This is probably the most interesting study since Haak et al. 2015 seven months ago.

It confirms what I wrote about the origins of the Basques in the Genetic history of the Spaniards and the Portuguese: (http://www.eupedia.com/genetics/spain_portugal_dna.shtml#basque)


The Baques are indeed somewhat different genetically from other Spaniards. They have a bit more Northwest European ancestry (inherited from Mesolithic hunter-gatherers), and completely lack Red Sea, Southwest Asian and Caucasian admixtures (see autosomal maps (http://www.eupedia.com/europe/autosomal_maps_dodecad.shtml)). The absence of Red Sea and Southwest Asian admixture indicates that the Basques do not have any Phoenician, Jewish, Greek, Roman or Arabic ancestry. Looking at maternal lineages, the Basques also stand out from the rest of the peninsula, lacking many haplogroups, be it those associated with African or Southwest Asian ancestry (HV, L, M1, U3, U6) or those linked to the original Indo-European homeland in Eastern Europe (H2a1, H4, H7, H8, H11, H15, I, T1a1a1, U2, U4, W). They make up for it with higher frequencies of Mesolithic and Neolithic lineages (H1, H2a2a, H3, H5a3, J2a1a, J1c, K1a, T2, U5, V and X). This is in perfect agreement with the fact that Basque language is non-Indo-European. What generally comes as a surprise is that 85% of Basque paternal lineages belong to the Proto-Celtic R1b-P312. This can be explained (http://www.eupedia.com/forum/threads/28386-How-did-the-Basques-become-R1b) by the fast replacement of male lineages due to warfare with neighbouring Proto-Celts and the establishment of a Celtic ruling class who quickly spread their Y-DNA through polygamy.

I very seriously doubt that any R1b-M269 will be found before 2500 to 3000 BCE at earliest, and not at high frequencies until 1500 to 2000 years ago, which is the TMRCA for the Basque R1b-M153. In all likelihood the Neolithic ancestors of the Basques belonged primarily to I2a1a (M26) and G2a and perhaps to a minority of E1b1b, J1, J2 and R1b-V88. Since this paper analysed samples dating from 3500 BCE to 1500 BCE, the more recent samples could already include R1b-M269, as PIE Bronze Age people had already reached France by 2500 BCE, Britain by 2200 BCE and and even central Iberia by 1800 BCE. On the other hand Atapuerca is is not so near from France and not in a region associated with early bronze cultures in Iberia, so it could very well be that no R1b-M269 shows up at all, even in samples from 1500 BCE.

Fire Haired14
08-09-15, 09:51
This is probably the most interesting study since Haak et al. 2015 seven months ago.

It confirms what I wrote about the origins of the Basques in the Genetic history of the Spaniards and the Portuguese: (http://www.eupedia.com/genetics/spain_portugal_dna.shtml#basque)



I very seriously doubt that any R1b-M269 will be found before 2500 to 3000 BCE at earliest, and not at high frequencies until 1500 to 2000 years ago, which is the TMRCA for the Basque R1b-M153. In all likelihood the Neolithic ancestors of the Basques belonged primarily to I2a1a (M26) and G2a and perhaps to a minority of E1b1b, J1, J2 and R1b-V88. Since this paper analysed samples dating from 3500 BCE to 1500 BCE, the more recent samples could already include R1b-M269, as PIE Bronze Age people had already reached France by 2500 BCE, Britain by 2200 BCE and and even central Iberia by 1800 BCE.

I just have a feeling the 3,500yo individuals will be of pure Neolithic decent and lack R1b. I'm not basing it on much it is just a hunch. We've already seen in Italy 3,900 years ago that was the case.

Brennos
08-09-15, 12:08
I just have a feeling the 3,500yo individuals will be of pure Neolithic decent and lack R1b. I'm not basing it on much it is just a hunch. We've already seen in Italy 3,900 years ago that was the case.

If you believe in bad luck, then R-M269 will pop up in early samples!:grin:

Brennos
08-09-15, 12:11
...so they are I2a like Motala?

No.Motala I2a is Mesolithic and not M26.

Sorry, I did a mistake.

So we haven't got any Y-DNA from Neolithic Scandinavia?

Angela
08-09-15, 16:44
Journalists almost always get it wrong to some extent. It's one thing to say that the Basques are the closest population to the El Portalon farmers, which should be no surprise by this point, and another thing to say there's no difference between the two. I'd be very surprised if there's been absolutely no gene flow into the Basques in all this time.

Also, a sample from even 3500 BC is not early Neolithic. So, that doesn't tell us what the farmers were like when they first arrived, yes? If the pattern is the same as for central Europe, there was very little admixture with HGs in the beginning, and then some admixture in the transition to the Middle Neolithic.

It will be interesting, of course, to see how the genomes might have changed from 3500 BC to 1500 BC. We do have an El Portalon genome from 2000 BC. See:
http://www.diva-portal.org/smash/get/diva2:667495/FULLTEXT01.pdf
Also see our discussion here about it.
http://www.eupedia.com/forum/threads/29796-4000BP-Iberian-farmer-clusters-with-Tuscans-not-Basque-or-Early-European-farmers?highlight=Portalon+farmer

It will be important to see if the two sets of researchers agree about the samples from that particular period.

Getting back to this paper, I see that Genetiker is claiming one of the samples, ATP3 is M269. The dating is very important. If this is a sample from 3500 BC it's a game changer. If it's from 2000 BC or 1500 BC, it could validate the steppe theory.

That comment about the 10-25% difference from other Iberians and it coming from the "east and North Africa" is interesting too if it actually appears in the paper. I don't know what they mean by "east". Do they mean steppe ancestry? Or do they mean Phoenician. I've always doubted there was a huge impact from Phoenicians, but there was, apparently, some migration from the east that can be seen in the

That comment about increased flow from North Africa is also interesting. I have been operating under the assumption that the North African percentages in Iberians was at least partly from the Neolithic, but this might show that's incorrect, and it's post Neolithic. However, perhaps it was once regionally substructured, and if and when we get genomes from Neolithic sites to the west, we'll find some.

Another interesting statement is the one that says the HG component is "local", and that the HG in the Neolithic farmers in Scandinavia is also "local" (SHG)* Isn't that directly contrary to the findings of the recent paper which said that the HG in their Iberian sample was closer to KO1 from central Europe than to La Brana?

Parenthetically, I floated the idea years ago that SHG might have spread westward and even southward, and might have been partly responsible for the increased HG in the transition from mid-to-late Neolithic Europe, and might also have been part of the reason for the increased ANE in Scots etc. because of the Scandinavian gene flow into them. That was met with great opposition. It will be interesting to see if it did happen.

*I got that wrong. The authors seem to feel that the SHG didn't contribute to anyone. Didn't Lazaridis and Haak say something similar? If I'm getting it right they're seeing Ajvide as contributing to the Scandinavian farmers.

bicicleur
08-09-15, 18:02
here you go :

https://genetiker.wordpress.com/2015/09/08/y-snp-calls-from-copper-and-bronze-age-spain/

3500-1500 BC, no specific date per sample

surprise, no I2a1a-M26 but I2a2a-M223

similar to what was found at Els Trock >5000 BC ?

Angela
08-09-15, 18:37
Well, it will be more interesting if the early samples are R1b M269. :)

Years ago, when we were still dealing with just modern YDna, I suggested that perhaps R1b moved west ahead of the main "Yamnaya" type steppe migrations. I had speculated that maybe R1b was a male mediated elite group that had moved into the Balkans and/or the Aegean very early, and that then the collapse of the late Neolithic civilizations forced some of these people westward.

I saw it as mostly a sea borne migration, moving into southern Italy and then onwards, with a major staging area somewhere around the Rhone. I think I based it on papers that came out around that time that showed a lot of R1b diversity from around the Rhone into the Alps.

All of the subsequent papers on ancient dna led me to abandon that theory.

I'd like to know the Ydna and autosomal signature of those people from Los Millares and Zambujal, who suddenly out of nowhere, around 2000 BC show evidence of very eastern Med type fortified cities etc.
https://en.wikipedia.org/wiki/Castro_of_Zambujal
https://en.wikipedia.org/wiki/Los_Millares

http://www.academia.edu/2923221/Social_Complexity_in_Copper_Age_Southern_Iberia_ca ._3200-2200_Cal_B.C._Reviewing_the_State_Hypothesis_at_Va lencina_de_la_Concepci%C3%B3n_Seville_Spain_

bicicleur
08-09-15, 19:35
I'd like to know the Ydna and autosomal signature of those people from Los Millares and Zambujal, who suddenly out of nowhere, around 2000 BC show evidence of very eastern Med type fortified cities etc.
https://en.wikipedia.org/wiki/Castro_of_Zambujal
https://en.wikipedia.org/wiki/Los_Millares

http://www.academia.edu/2923221/Social_Complexity_in_Copper_Age_Southern_Iberia_ca ._3200-2200_Cal_B.C._Reviewing_the_State_Hypothesis_at_Va lencina_de_la_Concepci%C3%B3n_Seville_Spain_

if i recall well Los Millares is >3000 BC
it would be interesting, i wouldn't expect either of both R1b-M269

I'd also like to know La Bastida / El Argar culture +/- 2000 BC, first bronze in Iberia

Fire Haired14
08-09-15, 20:06
The R1b1a2 is from 3516–3362 BC. The paper is out (http://www.pnas.org/content/early/recent), his ID is ATP3. I have to be honest, this doesn't make any sense. Lets wait for more analysis by Genome bloggers.

arvistro
08-09-15, 20:11
The R1b1a2 is from 3516–3362 BC. The paper is out (http://www.pnas.org/content/early/recent), his ID is ATP3. I have to be honest, this doesn't make any sense. Lets wait for more analysis by Genome bloggers.
Crazy! No ANE Basque R1b 3500 BC...
Now, that is a rumour.

Sile
08-09-15, 20:12
Table 1 has the following ydna
S5.1. ATP2
ATP2 displayed the derived allele for nine Y chromosome markers (Table S5); with all of the
markers providing phylogenetic support for ATP2 belonging to haplogroup H2. These
markers included: L985, L1013 and L1053 (A1); M235, P159 and P187 (F); L279, L281 and
P96 (H2). Previously labeled haplogroup F3, H2 was recently redefined on the basis of an
overlap between the datasets of[64] and[65][63]. It was found that the two haplogroups, H-M69 and F3-M282,
shared a root defined by the marker M3035. While only a few H2
individuals have ever been found, the haplogroup appears to have a west Eurasian
distribution; with a low level Middle Eastern presence in modern-day Iran, Turkey, Bahrain,
Kuwait and Qatar (Family Tree DNA,[66]), as well as minor occurrences in modern-day
England, France, Sardinia, Sweden and the Netherlands (Family Tree DNA,[64,65,67]
). H2also seems to occur at low frequencies in Neolithic samples[68].

So Ydna of H2
and mtdna of U5b3


and other sample

S5.2. ATP12-1420
ATP12-1420 displayed the derived allele for five Y chromosome markers (Table S6); with all
of the markers providing phylogenetic support for ATP12-1420 belonging to haplogroup
I2a2a. These markers included: L1053 (A1); P124 (IJ); L460 (I2a); L34 and P221 (I2a2a).
While the almost European-specific haplogroup I arose approximately 20000 to 25000 years
ago[67,69], haplogroup I2a2a may have diverged as a subclade, around 15000 years ago
[69], possibly during the recolonization of Europe following the Last Glacial Maximum (LGM).
Unlike the more common subclades of I1 and I2a1, haplogroup I2a2a appears at relatively
low frequencies across much of Europe. Its highest levels (10-12%) are found in modern-day
Germany and the Netherlands, with frequencies of around 5%, notably occurring in parts of
modern-day France as well as Mordvin in the Volga region of central Eastern Europe[69].

ydna of I2a2a
mtdna of H3c

Fire Haired14
08-09-15, 20:19
I added the Copper age Spanish to Pre-Historic West Eurasian Phenotype (https://docs.google.com/spreadsheets/d/1xe9sgt0PSt6cUQ3cYp14foBoaVGsOKZBmmHJoKz0HB0/edit#gid=1798287387): 374F was still at low frequency, lactose intolerance, 3/3 Brown eyes, One was a carrier of Red hair.

Sile
08-09-15, 21:10
This might be a better paper for some

http://www.pnas.org/content/early/2015/09/02/1509851112.full.pdf?with-ds=yes

epoch
08-09-15, 21:23
This might be a better paper for some

http://www.pnas.org/content/early/2015/09/02/1509851112.full.pdf?with-ds=yes

At first sight they do NOT call R1b Y-DNA for ATP3

Angela
08-09-15, 22:16
The earliest date I've seen for Los Millares is about 3200 BC, so that's about a one hundred year difference from the date of this particular sample (latest date of 3362BC). However, the date from the paper is calibrated, I don't know about the general Los Millares date. I'll have to check.

The authors didn't publish a y dna clade for ATP3, probably because it's so low coverage, so all we have is that one call by Genetiker.

In terms of Neolithic people we seem to have found the blue eyed genes in Central Europe so far, yes? Interesting that they have the 24A5 but only a bit of the 42A5 in terms of pigmentation. Oetzi had both. What about Remedello? Do we know?

P.S. The authors do make it clear these are pre-Beaker.

Fire Haired14
08-09-15, 23:03
In terms of Neolithic people we seem to have found the blue eyed genes in Central Europe so far, yes? Interesting that they have the 24A5 but only a bit of the 42A5 in terms of pigmentation. Oetzi had both. What about Remedello? Do we know?

Everyone is low in 42A5 till Corded Ware. I didn't know Oetzi had both. One Remedello had CG(~2900 BC) and one CC(~2000 BC). A rise in 42A5 looks like a Pan-European event that didn't affect West Asia much. It looks like Blue eyes were higher in the Eastern/Northern(Hungary-Sweden) half of the Neolithic world and could be why the same divide exists today.

Brennos
08-09-15, 23:09
The earliest date I've seen for Los Millares is about 3200 BC, so that's about a one hundred year difference from the date of this particular sample (latest date of 3362BC). However, the date from the paper is calibrated, I don't know about the general Los Millares date. I'll have to check.

The authors didn't publish a y dna clade for ATP3, probably because it's so low coverage, so all we have is that one call by Genetiker.

In terms of Neolithic people we seem to have found the blue eyed genes in Central Europe so far, yes? Interesting that they have the 24A5 but only a bit of the 42A5 in terms of pigmentation. Oetzi had both. What about Remedello? Do we know?

P.S. The authors do make it clear these are pre-Beaker.

I see Genetiker link for that presumed R1b individual: he has many calls on multiple haplogroups! How is possible? I see Haplogroup Q, haplogroup E, haplogroup R... Perhaps Gemetiker hopped to hurry conclusions...

The authors give only two Y-DNA results.

Finalise
09-09-15, 01:53
I highly doubt M269/L23 will pop. Proponents of West Asian L23 theory say it was a Chalcolithic farming expansion from Anatolia to the Danube, not Cardial/LBK movements.I think LBK = G with some J2Cardial Ware = EV13, G, J2

Greying Wanderer
09-09-15, 04:22
Well, it will be more interesting if the early samples are R1b M269. :)

Years ago, when we were still dealing with just modern YDna, I suggested that perhaps R1b moved west ahead of the main "Yamnaya" type steppe migrations. I had speculated that maybe R1b was a male mediated elite group that had moved into the Balkans and/or the Aegean very early, and that then the collapse of the late Neolithic civilizations forced some of these people westward.

I saw it as mostly a sea borne migration, moving into southern Italy and then onwards, with a major staging area somewhere around the Rhone. I think I based it on papers that came out around that time that showed a lot of R1b diversity from around the Rhone into the Alps.

All of the subsequent papers on ancient dna led me to abandon that theory.

I'd like to know the Ydna and autosomal signature of those people from Los Millares and Zambujal, who suddenly out of nowhere, around 2000 BC show evidence of very eastern Med type fortified cities etc.
https://en.wikipedia.org/wiki/Castro_of_Zambujal
https://en.wikipedia.org/wiki/Los_Millares

http://www.academia.edu/2923221/Social_Complexity_in_Copper_Age_Southern_Iberia_ca ._3200-2200_Cal_B.C._Reviewing_the_State_Hypothesis_at_Va lencina_de_la_Concepci%C3%B3n_Seville_Spain_


Copper in places like Cyprus, Corsica, Iberia - seems likely they might have at least some sea contact with each other.

bicicleur
09-09-15, 09:54
The earliest date I've seen for Los Millares is about 3200 BC, so that's about a one hundred year difference from the date of this particular sample (latest date of 3362BC). However, the date from the paper is calibrated, I don't know about the general Los Millares date. I'll have to check.

The authors didn't publish a y dna clade for ATP3, probably because it's so low coverage, so all we have is that one call by Genetiker.

In terms of Neolithic people we seem to have found the blue eyed genes in Central Europe so far, yes? Interesting that they have the 24A5 but only a bit of the 42A5 in terms of pigmentation. Oetzi had both. What about Remedello? Do we know?

P.S. The authors do make it clear these are pre-Beaker.

afaik the walls of Los Millares collapsed and were rebuild 3025 BC
dates for the 1st construction of Los Millares are unknown

probably explorers where at first attracted by alluvial copper which maby natives had allready found
after they would have been looking for copper ores

don't know whether in Atapuerca it was the same situation

Taranis
09-09-15, 13:17
I'd like to say that a Late Neolithic origin for the Basques is very much compatible with the linguistic evidence: Proto-Basque was decisively not the language of Mesolithic hunter-gatherers, and given that its an isolate language, the notion "Basques were recent (Bronze Age) immigrants" decisively doesn't hold up. If the Beaker culture started out as a native, western European phenomenon (that only later got 'hijacked' by Indo-Europeans in Central Europe), as I recall Maciamo asserted a while back, it would also explain why Basque has its own vocabulary for metallurgy. Just saying. :smile:

Angela
09-09-15, 14:23
Everyone is low in 42A5 till Corded Ware. I didn't know Oetzi had both. One Remedello had CG(~2900 BC) and one CC(~2000 BC). A rise in 42A5 looks like a Pan-European event that didn't affect West Asia much. It looks like Blue eyes were higher in the Eastern/Northern(Hungary-Sweden) half of the Neolithic world and could be why the same divide exists today.

Maybe you were right to doubt...I went back to Keller et al 2012, and Otzi is derived for SLC24A5. I don't know where I got the idea he was derived for SLC 42A5. Did Genetiker run his genome for depigmentation snps?

I wouldn't necessarily say that everyone was low in SLC42A5 until Corded Ware. These are Genetiker's findings for 42A5:

I don't think these groups were low in it.
Motala 4/7 GG (derived), 2/7 CG Heterozygous, 1/7 CC ancestral
Karelia CG Heterozygous
Samara GG Derived

The early LBK had it, but at lower levels:
LBK EN 2/9 GG derived, 1/9 CG Heterozygous, 5/9 CC ancestral

I don't think these three groups are all that different:
Corded Ware 2/3 GG derived, 1/3 CG Heterozygous
Unetice 2/6 GG Derived, 3/6 GC Heterozygous, 1/6 CC derived
Bell Beaker 3/5 GG Derived, 1/5 CG Heterozygous, 1/5 CC ancestral

Do the studies agree on these snps?

The only MN results I saw on Genetiker were:
Baalberge: 2/2 CC Ancestral

Esperstedt:1/1 CG Heterozygous

Remedello (according to your data)
1/1 CG Heterozygous

Do you have any other results for MN samples?

I would say that European levels for 42A5 have risen everywhere, even in the far northeast, which would go to Mathiesen et al's point about selection within the last 5,000 years.

bicicleur
09-09-15, 14:27
what about the H2 individual ?

it has also be found in Starcevo



Starčevo
Hungary
Alsónyék-Bátaszék [BAM25]
M
5710-5550 BC
H2
L281+
markers for F: (P142+, P145+, P138+, P316+, P14+, P159+) Reported as F* in Szécsényi-Nagy
N1a1a1b, reported as N1a1 in
Szécsényi-Nagy
Szécsényi-Nagy 2014 (http://www.ancestraljourneys.org/bibliography.shtml#Szecsenyi-Nagy2014);Haak 2015 (http://www.ancestraljourneys.org/bibliography.shtml#Haak2015)



where did they come from ?
are there still H2 individuals among modern European ?
afaik the H in modern Europe are gipsies, they arrived just 1500 year ago and are not H2

Arame
09-09-15, 16:08
H2 is not Gypsy, Indian H is in H1

H2 is the ex F3-M282


ATP2 displayed the derived allele for nine Y chromosome markers (Table S5); with all of the
markers providing phylogenetic support for ATP2 belonging to haplogroup H2. These
markers included: L985, L1013 and L1053 (A1); M235, P159 and P187 (F); L279, L281 and
P96 (H2). Previously labeled haplogroup F3, H2 was recently redefined on the basis of an
overlap between the datasets of [64] and [65] [63]. It was found that the two haplogroups, HM69
and F3-M282, shared a root defined by the marker M3035. While only a few H2
individuals have ever been found, the haplogroup appears to have a west Eurasian
distribution; with a low level Middle Eastern presence in modern-day Iran, Turkey, Bahrain,
Kuwait and Qatar (Family Tree DNA, [66]), as well as minor occurrences in modern-day
England, France, Sardinia, Sweden and the Netherlands (Family Tree DNA, [64,65,67]). H2
also seems to occur at low frequencies in Neolithic samples [68].

Tomenable
09-09-15, 17:23
The paper says that El Portalon farmers assimilated relatively many hunter-gatherers:

http://www.pnas.org/content/early/2015/09/02/1509851112.full.pdf


the Chalcolithic El Portalón individuals additionally mixed with local southwestern hunter–gatherers. The proportion of hunter–gatherer-related admixture into early farmers also increased over the course of two millennia. The Chalcolithic El Portalón individuals showed greatest genetic affinity to modern-day Basques, who have long been considered linguistic and genetic isolates linked to the Mesolithic whereas all other European early farmers show greater genetic similarity to modern-day Sardinians

The same process of assimilation took place for example in northern parts of Europe:

http://www.anthrogenica.com/showthread.php?1646-Genome-of-a-late-Neolithic-Iberian-farmer&p=107781&viewfull=1#post107781


(...) Genome-wide comparisons show that a Funnel Beaker female from Sweden and contemporary farmers from Germany, despite being most closely related to early European farmers, had somewhat more hunter gatherer ancestry. The same is true of their probable source population in Hungary [LBK in Transdanubia], and indeed farmers in Spain between 4000 and 3000 BC. It seems that as farmers extended their territory, they absorbed some of the foragers who were being pushed to the fringes and ultimately to the extinction of their way of life. (...)

Angela
09-09-15, 17:58
If memory serves, there's some of this H2 (formerly F3) in Sardinia. I think it's in the Francalacci paper.

Sile
09-09-15, 20:28
If memory serves, there's some of this H2 (formerly F3) in Sardinia. I think it's in the Francalacci paper.

there is also one in the hungarian samples

Sile
09-09-15, 20:30
what about the H2 individual ?

it has also be found in Starcevo



Starčevo
Hungary
Alsónyék-Bátaszék [BAM25]
M
5710-5550 BC
H2
L281+
markers for F: (P142+, P145+, P138+, P316+, P14+, P159+) Reported as F* in Szécsényi-Nagy
N1a1a1b, reported as N1a1 in
Szécsényi-Nagy
Szécsényi-Nagy 2014 (http://www.ancestraljourneys.org/bibliography.shtml#Szecsenyi-Nagy2014);Haak 2015 (http://www.ancestraljourneys.org/bibliography.shtml#Haak2015)



where did they come from ?
are there still H2 individuals among modern European ?
afaik the H in modern Europe are gipsies, they arrived just 1500 year ago and are not H2

for a very rare ydna marker, these H2 have been popping up everywhere in ancient europe

Sile
09-09-15, 20:32
Maybe you were right to doubt...I went back to Keller et al 2012, and Otzi is derived for SLC24A5. I don't know where I got the idea he was derived for SLC 42A5. Did Genetiker run his genome for depigmentation snps?

I wouldn't necessarily say that everyone was low in SLC42A5 until Corded Ware. These are Genetiker's findings for 42A5:

I don't think these groups were low in it.
Motala 4/7 GG (derived), 2/7 CG Heterozygous, 1/7 CC ancestral
Karelia CG Heterozygous
Samara GG Derived

The early LBK had it, but at lower levels:
LBK EN 2/9 GG derived, 1/9 CG Heterozygous, 5/9 CC ancestral

I don't think these three groups are all that different:
Corded Ware 2/3 GG derived, 1/3 CG Heterozygous
Unetice 2/6 GG Derived, 3/6 GC Heterozygous, 1/6 CC derived
Bell Beaker 3/5 GG Derived, 1/5 CG Heterozygous, 1/5 CC ancestral

Do the studies agree on these snps?

The only MN results I saw on Genetiker were:
Baalberge: 2/2 CC Ancestral

Esperstedt:1/1 CG Heterozygous

Remedello (according to your data)
1/1 CG Heterozygous

Do you have any other results for MN samples?

I would say that European levels for 42A5 have risen everywhere, even in the far northeast, which would go to Mathiesen et al's point about selection within the last 5,000 years.

Genetiker did all of the Haak samples for hair and eye colour on his site

Fire Haired14
09-09-15, 20:38
Maybe you were right to doubt...I went back to Keller et al 2012, and Otzi is derived for SLC24A5. I don't know where I got the idea he was derived for SLC 42A5. Did Genetiker run his genome for depigmentation snps?

No but I'll ask him to get calls for Otzi.


I wouldn't necessarily say that everyone was low in SLC42A5 until Corded Ware.

You're right. We don't have a whole lot a data and Ancient DNA has thrown out surprises before.



Do the studies agree on these snps?

I emailed the lead author Iain Mathieson of the paper "Eight thousand years of natural selection in Europe (https://www.google.com/url?sa=t&rct=j&q=&esrc=s&source=web&cd=1&cad=rja&uact=8&ved=0CB4QFjAAahUKEwi11pvey-rHAhUQe5IKHXl6AQg&url=http%3A%2F%2Fbiorxiv.org%2Fcontent%2Fearly%2F2 015%2F03%2F13%2F016477&usg=AFQjCNH1Z6LwbdTOi-SO72q9ZoxZ1jFyyA&sig2=xM2kXV2zQuu2dja48TgJBQ&bvm=bv.102022582,d.aWw)"and asked him if Geneticker's results are correct. And he said all the results look correct. Genome bloggers converted much of the data of ancient DNA from Haak and Allentoft into 23andme format, and I looked at the calls. I think only a few times they dis agreed with Geneticker.


Do you have any other results for MN samples?


No

Sile
09-09-15, 20:46
Since portalon matches ancient etruscans and I now think etruscans did not come from Anatolia from the lydians ( lydians fought phyrians in 500BC in central anatolia and no mention of association by greek writers of lydians with Etruscans from this written war was noted) , can there be a possibility that some of these ancient portalon basques migrated to Italy?

bicicleur
10-09-15, 09:16
for a very rare ydna marker, these H2 have been popping up everywhere in ancient europe

I suspect their origin is paleolithic India and they survived LGM in SW Asia.
Then they came along with farmers/herders to Europe.
Are there still H2 in India?

Arame
10-09-15, 09:21
There is no data about H2 in India.

There are H2 in England, France, Sweden. Also Sardinia. One Armenian from Turkey, and an Assyrian from Iran. Also 3 person from Kuwait/Qatar.

H2 is the F-M282
https://www.familytreedna.com/public/F-YDNA/default.aspx?section=yresults

The split between H2 and H1 happened some 35.000-45.000 ybp.
H1 is in India.

Alan
10-09-15, 14:16
Crazy! No ANE Basque R1b 3500 BC...
Now, that is a rumour.


Thats not crazy, thats just what I tried to explain the people in the comment section of Eurogenes. R1b is a far too old Haplogroup. By Neolithic , R1b must have spred around West, Central Asia and the Steppes already with completely different autosomal DNA. Some R1b (such as V88) reached the Levant with EEF ancestry and no sign of ANE other R1b such as found among the Samara EHG had completely different autosomal DNA and R1b (M343, l23) might have been widesred among teal eastern farmers.

Arame
10-09-15, 14:46
Alan

But according to Genetiker who found this R1b ( it was absent from the study ) the ATP3 has a Caucasian admixture.
BTW the paper also lacks an admixture run for ATP3. Maybe it was considered too low coverage.

I agree with You that R1b is old. So they could have different admixtures in various places. But the Z2103 and L51 are not old.
This ATP3 is has no call for L23 and L51.



ATP3, Pre-Beaker Copper Age, 3516–3362 BC


32.47% Southern-European-Caucasoid
31.97% Northern-Middle-Eastern-Caucasoid
14.04% Northern-European-Caucasoid
6.34% European-hunter-gatherer-Caucasoid
5.75% Bushman-and-Pygmy
3.82% Veddoid-Caucasoid-hybrid
3.55% Southern-Middle-Eastern-Caucasoid
2.05% Western-Negroid
0.01% Taiwanese-aborigine-Mongoloid
0.00% Australoid
0.00% Eastern-Negroid
0.00% Eskimo
0.00% Itelmen-and-Koryak
0.00% Northern-Amerindian
0.00% Northern-Mongoloid
0.00% Southern-Amerindian
0.00% Southern-Mongoloid

Alan
10-09-15, 16:50
Alan

But according to Genetiker who found this R1b ( it was absent from the study ) the ATP3 has a Caucasian admixture.
BTW the paper also lacks an admixture run for ATP3. Maybe it was considered too low coverage.

I agree with You that R1b is old. So they could have different admixtures in various places. But the Z2103 and L51 are not old.
This ATP3 is has no call for L23 and L51.

Yes ATP3 is m269 which is ancestral to l23. So yes no doubt it has heavy Caucaso_Gedrosian admixture. But I was talking about the 5000 year old Neolithic Iberian sample which is most likely R1b V88 and he was typically EEF.

So as I said R1b was widespred on the whole globe and I believe it ultimately started off somewhere between the Iranian Plateau and SouthCentral Asia as something Kalash like. mixing with farmer DNA and becoming Teal component. Some of it moved North to Eastern H&G and became EHG (Aren't there signs of Gedrosia admixture in EHG too?). Anothzer major wave moved deeper into Western Asia where a branch of it (V88) moved into levant and assimilated into the EEF culture. Other branches (m343, m269 and downstream clades) stayed among their Teal(Eastern Farmer) cousins in Kurdistan/Armenia/Azerbaijan/Iran and moved into the Caucasus/Maykop Culture (L23) From there they mixed with the Eastern Hunter and Gatherers and became Yamna. Since Yamna R1b is very different from EHG R1b and there are thousands of years in between them.

Angela
10-09-15, 18:18
I'm not totally comfortable drawing a lot of definite conclusions from this Admixture analysis done by Genetiker. I'm not saying it's not an accurate representation of what the calculator shows, mind you. Does anyone know, by the way, who created this calculator, or how accurate it's been in analyzing high quality ancient genomes?

Which brings me to the point that some of these genomes, in particular ATP 3, are not high quality at all.

Also, I find the "African", not "North African" percentages in some of these samples quite startling:

ATP3 3500 BC, 2.05 WEST Negroid

ATP2 2900 BC, 12.47 W. Negroid, 1.42 E Negroid, 14.11 Bushman

ATP20 2300 to 2000 3.5 W Negroid, 4.46 E Negroid

ATP 9 Mid Bronze 1700 2.42 W Negroid, 1.49 E Negroid

I mean, this 2900 BC sample looks at least a quarter Sub Saharan. Do we think that's possible? Ancient EEF sometimes throw up a few percent SSA, like Otzi, for example, which might be noise given the age of the samples, but this much? It's true that the authors themselves say that they found evidence of African in these samples, but they sort of waffle on how much. If this calculator is accurate would it mean there was that much SSA in parts of Iberia from the time of the late Neolithic? Might it represent a movement up the west coast of Iberia or did some migration from the east stop off in North Africa and incorporate some SSA heavy people? I don't know. That's way too much speculation for me based on an amateur (?) calculator using less than optimum quality genomes.

Anyway, if we are going to try to get some clues from the calculator results, I think it may be more helpful to group them by time period and to show at least three of the most important components, Northern Middle East, Northern Euro, and "veddoid".

The results are in that order: Northern Middle East, Northern Euro, and Veddoid

ATP3 3500-3300: 31.97/14.04/3.82

ATP7 3300-2900: 0/18.73/3.82
ATP16 3200-2900: 8.17/12.65/0
ATP17 3000-2800: 11.14/7.33/0
Matojo 3000-2900: .01/15.97/.11

ATP2 2900-2600: 2.60/12.60/0

ATP20 2300-2000: 0/18.92/28.14

ATP9 Mid-Bronze 1750-1600: 3.21/26.32/0

Looking at the "North Euro" score, the only really clear pattern I see is that it is consistently higher in the period from 2300 BC, when it's 18.92, to 1700-1600 BC, when it reaches 26.32%. That makes sense to me. I think this component was always present because it's related to "Euro" hunter-gatherers, but it increased when there were movements into Iberia starting around 2000 with the beginning of the Bronze Age. ( I'm not sure what to make of the 14.04 in ATP3, but given it's one of the worst samples, I think caution is advised. You can also see that this score fluctuates wildly in the big chunk of Chalcolithic people from 3300 to 3,000, with one sample at 18.73, and another at 7.33.)

The "Veddoid" component is absent in the vast majority of these samples, including in the Bronze Age sample which we would think would best represent the new "Indo-European" element. Then we have the 3.82 in the ATP 3 sample, which is the oldest, and an anomalous 28.14 score in ATP 20 from 2300 to 2000 BC, the same sample that has absolutely 0 Northern Middle East. Either this component is very difficult to pin down, or the bad quality of the genomes makes it impossible to pin it down, or this calculator isn't very good at capturing it.

That leaves the Northern Middle East component, which really only makes up a substantial portion of the ATP 3 sample. (low quality as we said) It's at an extraordinary 31.97 level. The Chalcolithic block from 2200 to 3000 BC varies from 0 to 11.14. By 3000 BC it's way down in the single digits.

If I were forced to make a prediction, I would say that if ATP 3 is really R1b M269 then it represents a movement of at least some very Northern Middle Eastern like R1b people from the east into Iberia by 3500 BC (or earlier), whose signal was diluted by intermarriage with locals and then by mixing with "Indo-Europeans" entering Iberia from the north in the Bronze Age.

I'd also say that the Bronze Age invaders of Iberia had very little "Indo-European" left in them by that time if you define "Indo-European" as the Yamnaya.

All of this is only if I were FORCED to make a prediction, mind you. :) I'm not comfortable making predictions based on this kind of evidence.

bicicleur
10-09-15, 19:36
a simple question to put things in perspective : does ATP3 has ofspring today?
my rough guess : any random individual > 5000 yo has max 10 % chance to have ofspring today

Alan
10-09-15, 21:16
I'm not totally comfortable drawing a lot of definite conclusions from this Admixture analysis done by Genetiker. I'm not saying it's not an accurate representation of what the calculator shows, mind you. Does anyone know, by the way, who created this calculator, or how accurate it's been in analyzing high quality ancient genomes?

Which brings me to the point that some of these genomes, in particular ATP 3, are not high quality at all.

Also, I find the "African", not "North African" percentages in some of these samples quite startling:

ATP3 3500 BC, 2.05 WEST Negroid

ATP2 2900 BC, 12.47 W. Negroid, 1.42 E Negroid, 14.11 Bushman

ATP20 2300 to 2000 3.5 W Negroid, 4.46 E Negroid

ATP 9 Mid Bronze 1700 2.42 W Negroid, 1.49 E Negroid

I mean, this 2900 BC sample looks at least a quarter Sub Saharan. Do we think that's possible? Ancient EEF sometimes throw up a few percent SSA, like Otzi, for example, which might be noise given the age of the samples, but this much? It's true that the authors themselves say that they found evidence of African in these samples, but they sort of waffle on how much. If this calculator is accurate would it mean there was that much SSA in parts of Iberia from the time of the late Neolithic? Might it represent a movement up the west coast of Iberia or did some migration from the east stop off in North Africa and incorporate some SSA heavy people? I don't know. That's way too much speculation for me based on an amateur (?) calculator using less than optimum quality genomes.



I think some of it represents very archaic West Eurasian(farmer?) genes in SSA populations which we didn't knew off.
Logically the more ancient the genes the closer to the roots also.


If I were forced to make a prediction, I would say that if ATP 3 is really R1b M269 then it represents a movement of at least some very Northern Middle Eastern like R1b people from the east into Iberia by 3500 BC (or earlier), whose signal was diluted by intermarriage with locals and then by mixing with "Indo-Europeans" entering Iberia from the north in the Bronze Age.

What if those R1b with high teal represent a Indo European population not yet deluted by EHG ancestry in the Steppes? This would fit one of my theories that Yamna was a secondary homeland for the Indo European coming with the teal admixture from somewhere else.

Angela
10-09-15, 21:37
I think some of it represents very archaic West Eurasian(farmer?) genes in SSA populations which we didn't knew off.
Logically the more ancient the genes the closer to the roots also.



What if those R1b with high teal represent a Indo European population not yet deluted by EHG ancestry in the Steppes? This would fit one of my theories that Yamna was a secondary homeland for the Indo European coming with the teal admixture from somewhere else.

They might represent a population that fed into the steppe people, but I don't think they can be called the "Indo-Europeans" based on the data we have so far.

I still think that the "Indo-Europeans" were the Yamnaya people, although I'm ready to be persuaded otherwise by new data.

MOESAN
11-09-15, 00:02
Good "paper" Angela
I agree for the most; let's not forget today Basques is not the same as ancient geographically "Basques";
that said, I find very boring all these abstracts where we always find unprecise geographic terms as western or eastern and so one. Always I've the impression people are trying to sale washing stuff. And I cannot believe in pure EEF in Iberia nor in any other place. Other paper said Iberians Neolithic people were close to Center-Eastern Europe and they shared just a taste of (W)HG, but the same paper shows the Middle Neolithic people of Iberia (Spain, Cataluna and other places) are more "westwards" shifted and closer to old WHG than Early and Middle Neolithic men of Central and Eastern Europe, even more shifted than today Sardinians, at least in some plotting (I know, plottings ...) - so the HG admixture increase by time, or Iberian Neolithic people were not exactly the same as other Farmers, even if they shared a lot of common ancestry. concerning this (W?)(S?)HG we have to wait to be sure (question of DNA coverage?)...
for Y-R1b I have no religion even if I favour the Steppes orgin. But a Megalitihic origin (4000 BC) with subsequent Atlantic Bronze is not to be discarded. From where through where??? a 3000 BC alley of Neolithic megalithers and first I-Eans Y-R1b (doped by BBs?) could explain the demographic increase of this period and the later Atlantic Bronze
The today Basques show litlle of it but they have ANE, they have 'gedrosia', they share some mt-H and mt-U with North-Eastern European people, they have more HG in them: saying after that "Basques descend almost only from Neolithic people from Near-East" or something like that is going very far; or we are not giving the same meaning to names? We lack aDNA from Portugal (see the surveys showing already differences between Cantabria and Basque country ancient mt-DNA, mt-H stronger in West from Late Paleolithic but well present (about 50%) in Basque Mesolithic: the "neolithical' mtDNA came rather during Chalcolithic than Neolithic and more marked in the Ebro river region than in North stayed "archic"; mt H augmented again in Middle Ages at the depends of mt-U but also at the depends of "neolithical" mtDNA!

MOESAN
11-09-15, 00:22
I would say that European levels for 42A5 have risen everywhere, even in the far northeast, which would go to Mathiesen et al's point about selection within the last 5,000 years.[/QUOTE]



Interesting Angela, but what about the other: SLC 24A5? These so short time of selection seems to me a bit curious; the selection concept is confusing sometimes: if a mutation on a locus is enough to strongly lighten the skin, why an other mutation with the same effect would be so imperiously needed and selected? Selection is complicated in fact: but we can also figure out an other natural selective pressure acting upon a gene or genes, with different "task" but very close on the same chromosome? Linkage?

Greying Wanderer
11-09-15, 01:17
afaik the walls of Los Millares collapsed and were rebuild 3025 BC
dates for the 1st construction of Los Millares are unknown

probably explorers where at first attracted by alluvial copper which maby natives had allready found
after they would have been looking for copper ores

don't know whether in Atapuerca it was the same situation

one of the things I was thinking about early copper working is say for the sake of argument there were five levels of difficulty in extracting copper with level one sites being panning for it in streams or simply chiseling it out of exposed rock and levels two to five being progressively more difficult to reach then the first level one dudes might have traveled far and wide looking for level one sites before they were able to extract it from level two difficulty sites - and then the same again between difficulty level two and three.

A process like that might have made the spread very erratic.

Greying Wanderer
11-09-15, 01:26
"Angela: I would say that European levels for 42A5 have risen everywhere, even in the far northeast, which would go to Mathiesen et al's point about selection within the last 5,000 years."



Interesting Angela, but what about the other: SLC 24A5? These so short time of selection seems to me a bit curious; the selection concept is confusing sometimes: if a mutation on a locus is enough to strongly lighten the skin, why an other mutation with the same effect would be so imperiously needed and selected? Selection is complicated in fact: but we can also figure out an other natural selective pressure acting upon a gene or genes, with different "task" but very close on the same chromosome? Linkage?

One possibility might be a mashup of the various theories.

Say lighter (but not light) skin had an advantage in northern Eurasia (or interior northern Eurasia) and so multiple depigmentation genes developed among separate populations in that region.

Say for the sake of argument there were five separate ones in total and they'd spread around a bit for the same reason they developed or a different reason until say most of the people who had them had 3 out of the 5.

Then farming either magnified the (or one of the) original selection pressures or added a second (or third) selection pressure on top.

Just an idea.

Angela
11-09-15, 02:20
Interesting Angela, but what about the other: SLC 24A5? These so short time of selection seems to me a bit curious; the selection concept is confusing sometimes: if a mutation on a locus is enough to strongly lighten the skin, why an other mutation with the same effect would be so imperiously needed and selected? Selection is complicated in fact: but we can also figure out an other natural selective pressure acting upon a gene or genes, with different "task" but very close on the same chromosome? Linkage?[/QUOTE]

I don't recall any paper saying that one depigmentation mutation was enough to lighten the skin to, say, "European fair" levels. Rather, the way I understood it was that each one acted on a different part of the melanin making or transportation process, or rather with the disruption of the melanin making process, with each contributing a certain amount of the final depigmentation result.

In other words, the effect was cumulative.

These are two links that I just happened to have in my files. I've posted lots more on various threads.

https://en.wikipedia.org/wiki/SLC24A5

http://www.pubfacts.com/detail/26057890/Membrane-Associated-Transporter-Protein-MATP-Regulates-Melanosomal-pH-and-Influences-Tyrosinase-Acti

As for the Mathiesen et al paper, the time period discussed was actually the last 8,000 years. I don't see it as so terribly surprising that in 8,000 years a certain mutation could rise to fixation. Look at the lactase persistence gene. We find it in one Bell Beaker person in central Europe and in a few people in Iberia, and it's now at huge frequency levels in central, northern and northwestern Europe.

I'm not saying that it was all selection, by the way. I'm just saying I don't see why selection couldn't have had a part in it after the random mutation and perhaps some initial admixture with people bearing it.

I also think that the selection in terms of an 8,000 year time span looks more like an increase in SLC42A5 to me, as you say. SLC24A5 derived was at very high levels even in the earliest Neolithic. Given that the derived snps are fixed in the Near East as well I think there's some chance that it arose or at least was being selected for quite a bit before 8,000 years ago, just not in all human groups apparently.

It will be very interesting to see the phenotype snps in the ancient Anatolian farmers. If they weren't derived for SLC24A5 then the farmers must have picked the mutation up on the way into Europe. Then selection would take over.

Wait, didn't the abstract for an upcoming paper on the Greek Neolithic say that they were "dark"? Of course, we don't know what that means precisely, but maybe the farmers did pick up some depigmentation snps (SLC 42A5? SLC24A5? Both?) somewhere in Europe.

There's no percentage in spending too much time speculating. We should know in two weeks.

Fire Haired14
11-09-15, 03:46
@Angela,

The "dark skin" report in Greek Neolithic is probably a miss interpretation from the media. They've miss interpreted authors before, because it's not an interest/hobby of theirs. By Dark skin my guess is Greek Neolithic had little 374F.

JS Bach
11-09-15, 04:07
Does anyone know, by the way, who created this calculator, or how accurate it's been in analyzing high quality ancient genomes?



I suspect Genetiker probably made it. That's just my opinion based on reading his blogs, though. And I think it was just recently made, and will have to stand the test of time as to how well it will hold up. I'd much like to see these new genomes' results on Dienekes' and Davidski's calculators.

Anyway, awesome find! It sheds light on how accurate or inaccurate the history we've been told can be. Maybe the Bell Beakers spread R1b-L11 and much of our Western European languages/language components from Iberia.

Also perhaps of note is the Southern Middle Eastern component in ATP3 of 3.55%. I guess it may or may not have been brought there by R1b. Part of Gedrosia?

Fire Haired14
11-09-15, 05:35
Davidski is doing analysis of ATP3 and suspects he has some ANE. In Davidski's PCA of West Eurasia ATP3 clusters by Northern Spanish not Neolithic farmers. He'll probably post more on analysis of all El Portalons in the net few weeks.

Arame
11-09-15, 06:56
This is the PCA of ATP3

Here it is marked as Spain_CA

https://drive.google.com/file/d/0B9o3EYTdM8lQY2R2XzktRXZhUWs/view?usp=sharing

He is among Spanishs! Most probably it could have some ANE.

Alan
11-09-15, 07:04
Davidski is doing analysis of ATP3 and suspects he has some ANE. In Davidski's PCA of West Eurasia ATP3 clusters by Northern Spanish not Neolithic farmers. He'll probably post more on analysis of all El Portalons in the net few weeks.

If Atp3 has modern Northern Middle Eastern/Caucaso-Gedrosia genes, of course he will have ANE, Since it's the decisive difference between western and eastern/teal farmrs. No need for suspections there.

Angela
11-09-15, 18:26
This is the PCA of ATP3

Here it is marked as Spain_CA

https://drive.google.com/file/d/0B9o3EYTdM8lQY2R2XzktRXZhUWs/view?usp=sharing

He is among Spanishs! Most probably it could have some ANE.

I'm having trouble deciphering it. Which precise Spanish group is he closest to?

MOESAN
11-09-15, 20:32
@Angela: OK, maybe I rised too quickly my voice!
but It's pity I've not the today distribution of mutated genes at SCL45A2
I've only maps about CL24A5 111*A, OCA2 355*, ASIP 8818*A, MATP 374*C and TYR 192*A
concerning skin colour, the only making total sense among these 5 is the SCL24A5, typically "europoid" and checking very well perceived skin pigmentation distribution -
none of the others 4 show a strong correlation to skin pigmentation among Europoids so they could be of little importance in depigmentation among them but ASIP 8818*A seems having a strong enough effect for light skin among 'mongolid' East Asians which lacked SCL24A5 mutated for the most- (the higher scores among Amerindians: North Siberian in origin?)
ASIP 8818 mutated is found too at low enough levels in some SSA groups as OCA2 mutated - this OCA2 mutated is strong enough among East Asians (not too much in America) and it seems that the cumulative effect of ASIP and OCA2 mutated genes was necessary to lighten the East Asians skin, even it this lightening is not completley as strong as among european 'europoids' (confirmed by the fact SSA people are not very fair skinned spite they have a bit!): so I suppose these 2 last mutations had a very less strong imput on skin pigmentation, compared to SCL24A5 mutation.
all that doesn't tell us anything about the SCL45A2 mutation penetration, helas for our question;
selection? YES! but principally for what mutated gene? ( Orcadians (fair skinned I suppose) and North Russians with lower %s of mutated genes at ASIP, OCA2, and TYR than some southern Europeans and others darker skinned groups...

to come back to the thread: all that SSA DNA in Iberia seems a problem of calculator at first sight even if we cannot discard other but surprising explanations (very mobile elite) - an archaic DNA seems amazing at these dates at a so high level!)
sorry it's the my aperitive time! Good lick!

Angela
11-09-15, 23:18
@Angela: OK, maybe I rised too quickly my voice!
but It's pity I've not the today distribution of mutated genes at SCL45A2
I've only maps about CL24A5 111*A, OCA2 355*, ASIP 8818*A, MATP 374*C and TYR 192*A
concerning skin colour, the only making total sense among these 5 is the SCL24A5, typically "europoid" and checking very well perceived skin pigmentation distribution -
none of the others 4 show a strong correlation to skin pigmentation among Europoids so they could be of little importance in depigmentation among them but ASIP 8818*A seems having a strong enough effect for light skin among 'mongolid' East Asians which lacked SCL24A5 mutated for the most- (the higher scores among Amerindians: North Siberian in origin?)
ASIP 8818 mutated is found too at low enough levels in some SSA groups as OCA2 mutated - this OCA2 mutated is strong enough among East Asians (not too much in America) and it seems that the cumulative effect of ASIP and OCA2 mutated genes was necessary to lighten the East Asians skin, even it this lightening is not completley as strong as among european 'europoids' (confirmed by the fact SSA people are not very fair skinned spite they have a bit!): so I suppose these 2 last mutations had a very less strong imput on skin pigmentation, compared to SCL24A5 mutation.
all that doesn't tell us anything about the SCL45A2 mutation penetration, helas for our question;
selection? YES! but principally for what mutated gene? ( Orcadians (fair skinned I suppose) and North Russians with lower %s of mutated genes at ASIP, OCA2, and TYR than some southern Europeans and others darker skinned groups...

to come back to the thread: all that SSA DNA in Iberia seems a problem of calculator at first sight even if we cannot discard other but surprising explanations (very mobile elite) - an archaic DNA seems amazing at these dates at a so high level!)
sorry it's the my aperitive time! Good lick!

Well, it's mine in a few minutes (Although I have to cook as I drink it!) so I'll be brief. :)

I posted the derived and ancestral results for SLC42A5 for the ancient samples upthread.

This is a chart from Lucotte et al of modern percentages of derived SLC42A5 by city. Not great, but better than nothing.
7410
7411
.
There is a map of the distribution of derived SLC42A5 in this post by Razib Khan:
http://blogs.discovermagazine.com/gnxp/2013/03/pigmentation-the-simplest-of-complex-traits-not-so-simple/#.VfNEm5dvBT8

Ed. The Lazaridis paper will be read in a few weeks so we'll know whether the farmers came into Europe with derived SLC24A5


(http://blogs.discovermagazine.com/gnxp/2013/03/pigmentation-the-simplest-of-complex-traits-not-so-simple/#.VfNEm5dvBT8)

Angela
11-09-15, 23:20
If Atp3 has modern Northern Middle Eastern/Caucaso-Gedrosia genes, of course he will have ANE, Since it's the decisive difference between western and eastern/teal farmrs. No need for suspections there.

I really don't think tremendous weight should be put on such a low coverage genome. It might give us some hints, but that's about it, in my opinion. That's probably the reason why the authors didn't even include ATP3 on their PCAs.

As to the source of the ANE, you may indeed be correct. I tend to think that people in the northeastern Near East may have had ANE before the arrival of any people from the steppe. Perhaps some of it, in fact, went onto the steppe from that region. When the Reich Lab gets done with all those samples from the Caucasus and surrounding areas we should have a much clearer picture.

I've also felt for a long time that later migrations of farmers into Europe from the Near East might have carried a bit of it as the ANE admixed Near Easterners moved slowly west. I can't remember now, but didn't Otzi have a smidgeon of West Asian in one of the calculators? Also, if people are so eager to do runs on ancient genomes, why has no one analyzed Barcin?

Therefore, I don't think it's a given that the ANE in this sample necessarily came from an EHG person. I'm also disinclined to give temendous weight to amateur generated analysis given all the confusion about ENF versus EEF. It would have been much better, in my opinion, to have waited for an actual genome from Anatolia.

IF this person is an admixed individual, part new arrival, part "local" Neolithic type, and not a migrant himself, the "father" or actual migrant must have had a heck of a lot of northern Middle East.

As to how he got to Iberia, I have some doubt that this individual, even if it's proved that he has a "Yamnaya" kind of autosomal signature, would have ridden a horse from the steppe across a mostly forest covered European landscape at a time when the horse hadn't even been domesticated yet, or was just being domesticated (see Anthony for a date about 3500 BC), and the later Corded Ware people still often used oxen to pull their primitive carts. Not to mention the fact that they would have had no reason to go due west on the European landmass to Iberia, leaving no trace of their passage in the Copper Age cultures of central Europe.

I think it's probably more likely that any travelers from the east would have sailed along already well established sea routes, used in the copper trade and prospecting at the time, and by interlocking obsidian networks before that, and the neolithic farmers before that. The sea routes were always the same because the winds and sea tides were generally the same.

Given all of that, I would tend to think that this original migrant, if he came around or just prior to this time, would more likely have departed from somewhere around the Balkans, or possibly the Aegean, perhaps with the collapse of the copper age cultures around the Balkans from either environmental collapse and/or pressure from the steppe. That's if he didn't arrive even earlier...

As to the objections that he's too early for the Copper Age in Iberia, I really don't see that. I did a little digging and there are some new texts on the whole topic of metallurgy.
https://books.google.com/books?id=Q0u-BAAAQBAJ&pg=PA425&lpg=PA425&dq=hunt+ortiz+et+al+2003+metallurgy/copper&source=bl&ots=xpU2fbV1Co&sig=PzjefHLHSmfTpL12eYj5BPVqe40&hl=en&sa=X&ved=0CB4Q6AEwAGoVChMI8O-32ZzqxwIVzBY-Ch2ngAv0#v=onepage&q=hunt%20ortiz%20et%20al%202003%20metallurgy%2Fcop per&f=false

They don't contradict previous findings that intensive copper ore extraction was going on at Monte Loreto in Liguria from the mid fourth millennium BC (Maggi and Pearce, 2005). Copper objects are found in Arene Candide in the late 5th millennium BC. Copper production, not objects, is apparent in Sardinia at the same time, in the latter part of the 5th millennium.

In Iberia itself, the mine at isn't attested until . However, the author of the above text maintains that copper smelting was going on in Iberia in the late 4th millennium BC going on until the early 3rd millennium BC. There is even fragmentary evidence of copper oxide slag at Cerro Virtud in SE Spain radio carbon dated to the first half of the 5th millennium BC (Montero Ruiz 1999) The author does recommend caution with this result because it is one millennium earlier than many of the others. Unfortunately, it seems to be the case, according to him, that likely sites are not being actively investigated, and/or are not secure.
http://www.qub.ac.uk/sites/EarlyMiningintheLowerSeguraValleySESpain/Image,280457,en.jpg

If any analysis is done despite the fact it's so low coverage I hope it's compared to a lot of ancient genomes to get a better handle on this, including the prior Portalon genome that plotted near modern day Tuscans, especially if that's a different genome than the ones analyzed in this paper. Actually, if it's the same genome or genomes, we need to know why it's plotting differently, if in fact it is....

Fire Haired14
11-09-15, 23:56
@Everyone,

BTW, my Dad lacks the two "Lactose Tolerant" mutations and he's drank milk his whole life with no problems. No one has questioned the effect of those mutations. There are certainly other factors involved. The same is true for skin color. More factors are involved than the SNPs rs1426654 and rs16891982. I'm sure they make decent affects though.

The easiest way to figure it out is looking at ancestry. All Europeans are mostly EEF/WHG+Steppe, including Greeks. West Asians appear to have little of such ancestry. So, somewhere in the EEF/WHG and Steppe world is where the Light skin comes from. The confusing thing is EEF/WHG and Steppe were as differnt from each other as West Asians and Europeans are today. So, it's hard to imagine it comes from both, but maybe.

It's probably a very complicated origin. Because Basque for example have Light skin and little Steppe-blood and Scythian had Light skin and had little EEF/WHG ancestry.

Greying Wanderer
12-09-15, 00:55
The author does recommend caution with this result because it is one millennium earlier than many of the others. Unfortunately, it seems to be the case, according to him, that likely sites are not being actively investigated, and/or are not secure.
http://www.qub.ac.uk/sites/EarlyMini...,280457,en.jpg (http://www.qub.ac.uk/sites/EarlyMiningintheLowerSeguraValleySESpain/Image,280457,en.jpg)

Interesting on that map that the gold and silver mining sites - which I assume came first - are located away from the copper sites in the Pyrenees implying that miners would have had to move to those sites from elsewhere - maybe from Iberia, maybe not.

copper rush? miner 4049-er (BC)

Sile
12-09-15, 02:45
As to how he got to Iberia, I have some doubt that this individual, even if it's proved that he has a "Yamnaya" kind of autosomal signature, would have ridden a horse from the steppe across a mostly forest covered European landscape at a time when the horse hadn't even been domesticated yet, or was just being domesticated (see Anthony for a date about 3500 BC), and the later Corded Ware people still often used oxen to pull their primitive carts. Not to mention the fact that they would have had no reason to go due west on the European landmass to Iberia, leaving no trace of their passage in the Copper Age cultures of central Europe.



agree with you on the horse


there is also some issues with Haak R1b-V88 in Spain

an interesting post

http://dispatchesfromturtleisland.bl...na-doesnt.html (http://dispatchesfromturtleisland.blogspot.com.au/2015/09/new-northern-iberian-ancient-dna-doesnt.html)

The H2, as discussed further below, is rare but has a generally West Eurasian non-hunter-gatherer distribution.

What About The Man From El Trocs Cave?
This said, there is one chink in this argument. In a 2015 paper by Haak et al., that reports 69 ancient DNA results from Europe, there is a reference to a man from Neolithic Spain ca. 5100 BCE whose body was found in the El Trocs cave in the Pyrenees Mountains in Northern Aragon whose Y-DNA haplogroup was found to be R1b1* ancestral to all extant forms of Y-DNA R1b (both V-88 from Africa and the Eurasian haplogroups; he is not R1b-V88 as has been frequently misreported). This long predates Bell Beaker and coincides with the very early Neolithic era in the region, and is also not far from modern Basque country.


IF not V88 , then another R1b from earlier than ATP3 in Iberia.

LeBrok
12-09-15, 04:23
@Everyone,

BTW, my Dad lacks the two "Lactose Tolerant" mutations and he's drank milk his whole life with no problems. No one has questioned the effect of those mutations. There are certainly other factors involved. The same is true for skin color. More factors are involved than the SNPs rs1426654 and rs16891982. I'm sure they make decent affects though.

I'm almost sure it has something to do with microbiota, bacterial flora quality in our gut, helping to digest everything, lactose included. Lactose persistence and digestion story is still not complete and not
fully understood.
Research reveals intolerance to be more common globally than lactase persistence, and that the variation has been tied to genetics, but that the largest source of variation has been shown to be based on exposure (e.g., cultures that consume dairy).
https://en.wikipedia.org/wiki/Lactose_intolerance

Fire Haired14
12-09-15, 07:16
Considering R1b-V88 and basal branches of R1b1a2 exist in West Asia it is no surprise to see both in Neolithic Europe.

Brennos
12-09-15, 15:54
agree with you on the horse


there is also some issues with Haak R1b-V88 in Spain

an interesting post

http://dispatchesfromturtleisland.bl...na-doesnt.html (http://dispatchesfromturtleisland.blogspot.com.au/2015/09/new-northern-iberian-ancient-dna-doesnt.html)

The H2, as discussed further below, is rare but has a generally West Eurasian non-hunter-gatherer distribution.

What About The Man From El Trocs Cave?
This said, there is one chink in this argument. In a 2015 paper by Haak et al., that reports 69 ancient DNA results from Europe, there is a reference to a man from Neolithic Spain ca. 5100 BCE whose body was found in the El Trocs cave in the Pyrenees Mountains in Northern Aragon whose Y-DNA haplogroup was found to be R1b1* ancestral to all extant forms of Y-DNA R1b (both V-88 from Africa and the Eurasian haplogroups; he is not R1b-V88 as has been frequently misreported). This long predates Bell Beaker and coincides with the very early Neolithic era in the region, and is also not far from modern Basque country.


IF not V88 , then another R1b from earlier than ATP3 in Iberia.

Is it El Troc 3 from Els Trocs? Is so, it is positive for the V88 equivalent SNP. On Ancestral Journeys, the site of Jean Manco, there is the result.

epoch
12-09-15, 16:55
Has the dating been verified? Could something have gone wrong there?

bicicleur
12-09-15, 17:12
agree with you on the horse


there is also some issues with Haak R1b-V88 in Spain

an interesting post

http://dispatchesfromturtleisland.bl...na-doesnt.html (http://dispatchesfromturtleisland.blogspot.com.au/2015/09/new-northern-iberian-ancient-dna-doesnt.html)

The H2, as discussed further below, is rare but has a generally West Eurasian non-hunter-gatherer distribution.

What About The Man From El Trocs Cave?
This said, there is one chink in this argument. In a 2015 paper by Haak et al., that reports 69 ancient DNA results from Europe, there is a reference to a man from Neolithic Spain ca. 5100 BCE whose body was found in the El Trocs cave in the Pyrenees Mountains in Northern Aragon whose Y-DNA haplogroup was found to be R1b1* ancestral to all extant forms of Y-DNA R1b (both V-88 from Africa and the Eurasian haplogroups; he is not R1b-V88 as has been frequently misreported). This long predates Bell Beaker and coincides with the very early Neolithic era in the region, and is also not far from modern Basque country.


IF not V88 , then another R1b from earlier than ATP3 in Iberia.

this is what I have



Spain
Els Trocs [Troc3]
M
5178-5066 BC
R1b1c
M415+, M343+, [L754 equivalent: L774/PF6245/YSC277+, PF1144+, V88 eqivalent: PF6376+]
M478-, PF6399-, L265-, L150-, M269-, V35-, V69-
pre-T2c1d2
Haak 2015; personal comm Sergey Malyshev, review of Y-DNA raw data

Finalise
12-09-15, 20:24
I don't know how some people can still view L23->L51 at the heart of the IE expansions even after all the evidence. R1a's connection to IE speakers is undisputed after Sintasha findings, modern high R1a frequencies in South Asia and their link to Corded Ware. L23->Z2103 is found in steppe at high frequencies and it is prevalent in Western Asia, Balkans, Eastern Europe where IE languages are spoken.L51 is nowhere to be found around the steppe, and the most likely scenario is that L23's homeland is around Eastern Anatolia, with the northern branch of Z2103 being the Maykops/Steppe people, and the western branch of L51 being the farming branch that travels through the Danube to western Europe. El Portalon just confirms this.

bicicleur
12-09-15, 21:55
I don't know how some people can still view L23->L51 at the heart of the IE expansions even after all the evidence. R1a's connection to IE speakers is undisputed after Sintasha findings, modern high R1a frequencies in South Asia and their link to Corded Ware. L23->Z2103 is found in steppe at high frequencies and it is prevalent in Western Asia, Balkans, Eastern Europe where IE languages are spoken.L51 is nowhere to be found around the steppe, and the most likely scenario is that L23's homeland is around Eastern Anatolia, with the northern branch of Z2103 being the Maykops/Steppe people, and the western branch of L51 being the farming branch that travels through the Danube to western Europe. El Portalon just confirms this.

you're a psychich

a lot of new data is going to follow the next few years

MOESAN
12-09-15, 22:17
@Angela: thanks for communication - I hope your drink was good, I'm rather statisfied by my one. I 'll look at all that. Good evening.

Brennos
12-09-15, 22:46
I don't know how some people can still view L23->L51 at the heart of the IE expansions even after all the evidence. R1a's connection to IE speakers is undisputed after Sintasha findings, modern high R1a frequencies in South Asia and their link to Corded Ware. L23->Z2103 is found in steppe at high frequencies and it is prevalent in Western Asia, Balkans, Eastern Europe where IE languages are spoken.L51 is nowhere to be found around the steppe, and the most likely scenario is that L23's homeland is around Eastern Anatolia, with the northern branch of Z2103 being the Maykops/Steppe people, and the western branch of L51 being the farming branch that travels through the Danube to western Europe. El Portalon just confirms this.

I'm sorry, but I can't agree: we have M269 in Neolithic Spain (M269 with no sub-clades recognized), and we have M269 with subclades in Eastern Europe (L23 and Z2103). Then, how can the M269 guy from Spain develop, in the same time but at the very end of a continent, the same mutation of L23 that is found in Eastern Europe to give life to the millions of Non-IE West Europeans? If so, it could easily be the greatest coincidence in Universe.

Another thing: M269 is a old branch, so it could easily take part to Neolithic migrations towards Europe. The answer lies in L23, L51 and L11 mutations. The steppe west of Don hasn't been sampled yet. So, El Portalon doesn't confirm a migration of L51 people... it confirms a migration of M269* people. I suppose that it is a different thing.

The last thing I would say is that we are so blind when speaking of Indoeuropeans that only a way must be opened: the northern one. All people claim Uralic and IE closeness, but we could also see a relationship between IE and Caucasian languages and also Semitic languages. I'm prone to think about a more southern homeland of PIE forefathers.

Angela
12-09-15, 22:47
I don't know how some people can still view L23->L51 at the heart of the IE expansions even after all the evidence. R1a's connection to IE speakers is undisputed after Sintasha findings, modern high R1a frequencies in South Asia and their link to Corded Ware. L23->Z2103 is found in steppe at high frequencies and it is prevalent in Western Asia, Balkans, Eastern Europe where IE languages are spoken.L51 is nowhere to be found around the steppe, and the most likely scenario is that L23's homeland is around Eastern Anatolia, with the northern branch of Z2103 being the Maykops/Steppe people, and the western branch of L51 being the farming branch that travels through the Danube to western Europe. El Portalon just confirms this.

How do you know that the L51 spread with the Neolithic? Why couldn't L51 have developed from the steppe R1b and then gone up the Danube? Wasn't there one R1b in Yamnaya that was ancestral to European lineages? Even if that isn't the case, how do we know that a related lineage ancestral to western European R1b wasn't further west?

R1b is very old. Some of it was apparently Neolithic, some of it became largely African, some of it became Indo-European. Haplogroups don't come with a race or culture or linguistic stamp.

I'm not saying you're wrong; I'm just saying we have no way of knowing yet. I will say that I find it hard to believe that people in France are one third Yamnaya (Haak et al) if R1b didn't bring Yamnaya ancestry to western Europe. There isn't enough R1a to account for it.*
7414

Who knows, maybe the original "Indo-Europeans" were R1b people who were living south of the Caucasus originally. Even if it arose in Yamnaya, you could make an argument that the R1a people were just Indo-Europeanized hunter-gatherers.

You know, I just noticed something. The France south sample is really from Aquitaine. That's where they spoke a Basque related language until into the Roman era. I think it's because that area wasn't on the major sea routes. They have roughly the same amount of Yamnaya as the other French; the difference is the small amount of WHG. I wonder why?

Ed. There also isn't enough steppe specific mtDna to account for it.

Angela
12-09-15, 23:39
I'm almost sure it has something to do with microbiota, bacterial flora quality in our gut, helping to digest everything, lactose included. Lactose persistence and digestion story is still not complete and not
fully understood.
Research reveals intolerance to be more common globally than lactase persistence, and that the variation has been tied to genetics, but that the largest source of variation has been shown to be based on exposure (e.g., cultures that consume dairy).
https://en.wikipedia.org/wiki/Lactose_intolerance

I think you may be right, Le Brok; I have two copies of the lactase persistence gene and stopped being able to drink milk or eat lots of cheese ten years ago.

However, the fact remains that those alleles don't exist until rather late in human history, and yet now the frequency in certain parts of Europe is extraordinarily high. They must have some beneficial effect.

MOESAN
12-09-15, 23:58
to totally express themselves (impose their effects) some genes need the co-presence of other genes or the absence of kind of "antgonist" genes, I think; the link can can be broken down by crossing-overs after generations and generations, or "repared" by the same process?
some cases of different penetrance could explained by that?
the difficulties of medical genetics research is here to support that

Angela
13-09-15, 00:27
to totally express themselves (impose their effects) some genes need the co-presence of other genes or the absence of kind of "antgonist" genes, I think; the link can can be broken down by crossing-overs after generations and generations, or "repared" by the same process?
some cases of different penetrance could explained by that?
the difficulties of medical genetics research is here to support that

Perhaps, but I'm talking about going from eating very large amounts of cheese, butter, ice cream etc into mid-life and then from one day to the next being unable to handle it at all. It was like the tripping of a light switch.

Not to get too much into personal revelations, but it was at a time of great personal stress and there were other health issues at the same time. I think changes in body chemistry can alter the operation of a lot of genes.

Ed. It was Lillet, by the way. Tonight, Campari. I'm a creature of habit. :)

Sile
13-09-15, 00:53
this is what I have



Spain
Els Trocs [Troc3]
M
5178-5066 BC
R1b1c
M415+, M343+, [L754 equivalent: L774/PF6245/YSC277+, PF1144+, V88 eqivalent: PF6376+]
M478-, PF6399-, L265-, L150-, M269-, V35-, V69-
pre-T2c1d2
Haak 2015; personal comm Sergey Malyshev, review of Y-DNA raw data




did you see Haak paper for el-trocs3 in Iberia ......I0410
it states
could thus be designated R1b1*(xR1b1a1, R1b1a2, R1b1c2, R1b1c3).

R1b1c is V88, he states, tested and not V88 that's what the x means inside the bracket

LeBrok
13-09-15, 06:50
I think you may be right, Le Brok; I have two copies of the lactase persistence gene and stopped being able to drink milk or eat lots of cheese ten years ago.

However, the fact remains that those alleles don't exist until rather late in human history, and yet now the frequency in certain parts of Europe is extraordinarily high. They must have some beneficial effect.I agree, genes have major bearing on it. There might be an even further twist. What if your lactose tolerant variant genes are not expressed at all? Somehow got methylated, perhaps by way of epigenetics? You mentioned stress. It could have been also huge dose of antibiotics killing good microbiota?

Brennos
13-09-15, 08:39
did you see Haak paper for el-trocs3 in Iberia ......I0410
it states
could thus be designated R1b1*(xR1b1a1, R1b1a2, R1b1c2, R1b1c3).

R1b1c is V88, he states, tested and not V88 that's what the x means inside the bracket

He didn't test for V88: he tested the sample for V88 major subclades, i.e. V69 and V35, and resulted negative. However it tested positive for V88 equivalent SNP. The x mean that it is negative for specific subclades tested: so, R1b1c2 and R1b1c3... not R1b1c!

bicicleur
13-09-15, 10:59
did you see Haak paper for el-trocs3 in Iberia ......I0410
it states
could thus be designated R1b1*(xR1b1a1, R1b1a2, R1b1c2, R1b1c3).

R1b1c is V88, he states, tested and not V88 that's what the x means inside the bracket

see comment : Haak 2015; personal comm Sergey Malyshev, review of Y-DNA raw data

V88 was not tested in the paper, but later, Y-DNA was reviewed, V88 eqivalent: PF6376 was found positive

that makes him R1b1c(xR1b1c2, R1b1c3)

Angela
13-09-15, 17:16
I agree, genes have major bearing on it. There might be an even further twist. What if your lactose tolerant variant genes are not expressed at all? Somehow got methylated, perhaps by way of epigenetics? You mentioned stress. It could have been also huge dose of antibiotics killing good microbiota?

Sorry, I just deleted most of my post because it was too off topic and too personal. :)

I'll just say that everybody who grew up in the west has taken way too many antibiotics. I didn't take a particularly big dose at the time this happened. Probiotics help a bit, but not much.

The strange thing is that my mother, for example, who developed a taste for milk and sweets after moving here, never lost her ability to digest them, nor did my father ever have a problem with cheese. I'm the odd person out. :)

Maciamo
14-09-15, 13:09
One thing that still bothers me with this new paper is that the 5500-year old ATP3 sample is considered to be Chalcolithic, although I cannot find any evidence of copper metallurgy in the northern half of Spain (and in southern France) until 5000 to 4500 years ago. Are the authors absolutely certain of their dating ? It's not just extremely odd to find an R1b-M269 with high Caucaso-Gedrosian ancestry in this period, it also doesn't make sense that it belongs to a Chalcolithic culture, especially for a "caveman".

Angela and Fire Haired mentioned that the ATP3 genome has low resolution and that the African and Veddoid components identified by Genetiker are probably wrong. But all samples has unusually high non-European admixtures, especially sub-Saharan African ones. Does that mean that none of the samples has adequate resolution to be of any use ? If that was the case I wouldn't have ventured trying to interpret the historical significance of that data as they did in the paper. Better no data than wrong data.

Another possibility is that the genomes are reliable, but that Genetiker's admixtures aren't. However Fire Haired emailed the lead author Iain Mathieson, who said that the admixtures looked correct. If so, then we still have a lot to figure out to explain how Late Neolithic northern Iberians got so much African admixture and why it mostly disappeared in modern North Iberians. On the other hand, the Veddoid and Amerindian admixtures could be an older component related to Paleolithic North Asians belonging to haplogroups Q, R*, R1 or old subclades of R1b that ended in Western Europe during the Ice Age.

It's also very odd to find a Yamna-like component (Genetiker's 'North-European', which is based on Yamna samples) in all of the samples found at El Portalon, when none of the Neolithic samples so far had any of it.

Fire Haired14
14-09-15, 13:21
Another possibility is that the genomes are reliable, but that Genetiker's admixtures aren't. However Fire Haired emailed the lead author Iain Mathieson, who said that the admixtures looked correct.

Iain Mathieson was the lead author of another paper "8,000 years of Natural Selection in Europe". He said the SNP calls Geneticker got looked correct. I think you're right to suspect Geneticker's admixture test isn't reliable. The authors are reliable and they got Africa scores for modern Iberians but not for Ancient ones. No Neolithic or Mesolithic European genomes to date show signs of African admixture.

sparkey
14-09-15, 18:42
A couple of thoughts on the I2 since I'm just now seeing these (very interesting) new ancient Y-DNA results:

ATP17: I2 M223+ Y4450- Y6098- is very unusual nowadays. Y4450 is the common SNP to all major modern M223 branches (Cont, Isles, Roots, and some outliers as well). Y6098 covers all the remaining outliers I'm aware of, namely the smallish groups "Basics1" (Ethan Allen's haplogroup) and "Basics2". So to have neither of those SNPs is a good indication that we could be looking at an extinct branch of M223 in this ancient fellow.

Matojo: Surprisingly good coverage on this individual, with no real chance of a false positive. I2 M223>Y6098 puts them clearly into the Basics1/Basics2 outlier branch I mentioned above, and to further be S23680+ Y6099- means that they're not Basics1 (which is Y6099) but are instead probably Basics2. Unfortunately, they tested different SNPs than how the FTDNA M223 Project defines Basics2, but since that's the only significant other modern branch of Y6098 other than Basics1, it's probably a good assumption that S23680 is a Basics2 SNP. Yfull estimates S23680 to have a TMRCA of 8100 ybp, and the M223 Project gives a modern distribution of Basics2 that clearly leans toward Western and Southern Europe (Spain, Portugal, France, UK, Italy), quite unlike the more common I2 M223>Y4450 branch, which leans more to Northern/Central Europe.

Fire Haired14
14-09-15, 20:12
A couple of thoughts on the I2 since I'm just now seeing these (very interesting) new ancient Y-DNA results:

ATP17: I2 M223+ Y4450- Y6098- is very unusual nowadays. Y4450 is the common SNP to all major modern M223 branches (Cont, Isles, Roots, and some outliers as well). Y6098 covers all the remaining outliers I'm aware of, namely the smallish groups "Basics1" (Ethan Allen's haplogroup) and "Basics2". So to have neither of those SNPs is a good indication that we could be looking at an extinct branch of M223 in this ancient fellow.

Matojo: Surprisingly good coverage on this individual, with no real chance of a false positive. I2 M223>Y6098 puts them clearly into the Basics1/Basics2 outlier branch I mentioned above, and to further be S23680+ Y6099- means that they're not Basics1 (which is Y6099) but are instead probably Basics2. Unfortunately, they tested different SNPs than how the FTDNA M223 Project defines Basics2, but since that's the only significant other modern branch of Y6098 other than Basics1, it's probably a good assumption that S23680 is a Basics2 SNP. Yfull estimates S23680 to have a TMRCA of 8100 ybp, and the M223 Project gives a modern distribution of Basics2 that clearly leans toward Western and Southern Europe (Spain, Portugal, France, UK, Italy), quite unlike the more common I2 M223>Y4450 branch, which leans more to Northern/Central Europe.

Western-Southern M223 is largely I2a2a2-Y6098 like one of the Late Neolithic Spanish? Most assumed I2a1a1-M26 would be the main Neolithic lineage of Iberia, but left out I2a2a-M223 assuming it came with medieval migrations of Germans into Iberia. That was obviously a mistake as we can clearly see with most Middle Neolithic Iberians coming out M223+.

You can see here Ancient West Eurasian Y DNA (https://docs.google.com/spreadsheets/d/12G2cfjG0wHWarsl5bB99ridFmvUWzqlZfZ6_e_R6oIA/edit#gid=479090567). Interestingly there is only one example of I2(xI2a1-M37) from Early Neolithic Europe, but all of a sudden I2a2a-M223 has a strong presence in Middle/Late Neolithic Spain and Bronze age Hungary. There's also an example of I2a2a-M223 from Yamnaya. The Yamnaya and a single Bronze age Hungarian I2a2a were of good coverage and belonged to I2a2a1a2a2(Hungary) and I2a2a1b1b2(Yamnaya). Do you know where those versions of I2a2a-M223 are mostly found today?

I wonder if I2a2a-M223 made some type of expansion, which can explain it's high frequency in Middle/Late Neolithic Spain and Bronze age Hungary, and it's high frequency in Central Europe today as opposed to I2a1-P37, G2a, and F*(the three main lineages of Early Neolithic farmers).

sparkey
14-09-15, 20:49
You can see here Ancient West Eurasian Y DNA (https://docs.google.com/spreadsheets/d/12G2cfjG0wHWarsl5bB99ridFmvUWzqlZfZ6_e_R6oIA/edit#gid=479090567). Interestingly there is only one example of I2(xI2a1-M37) from Early Neolithic Europe, but all of a sudden I2a2a-M223 has a strong presence in Middle/Late Neolithic Spain and Bronze age Hungary. There's also an example of I2a2a-M223 from Yamnaya. The Yamnaya and a single Bronze age Hungarian I2a2a were of good coverage and belonged to I2a2a1a2a2(Hungary) and I2a2a1b1b2(Yamnaya). Do you know where those versions of I2a2a-M223 are mostly found today?

The Yamnaya sample is downstream of Cont3 (I2-M223>L701), which is the broadly most eastern of the M223 branches, although it still has some of the typical M223 Central European distribution in addition to presence in Eastern Europe, etc. The M223 Project at FTDNA calls the Yamnaya sample's subclade "Cont3b," and shows that it has a very wide distribution ranging from Britain to India, with samples from France, Switzerland, the Czech Republic, Georgia, and even Algeria as well. It's not an outlier branch in modern samples, it's a subclade of the more common Y4450 SNP.

I know of a sample from Hungary (RISE247) that seems to be I2-M223>L1228. Interestingly, that's "Basics2," probably the same (admittedly rather old) subclade as Matojo. Were you talking about that sample, or the one from Szécsényi-Nagy 2015, or both?


I wonder if I2a2a-M223 made some type of expansion, which can explain it's high frequency in Middle/Late Neolithic Spain and Bronze age Hungary, and it's high frequency in Central Europe today as opposed to I2a1-P37, G2a, and F*(the three main lineages of Early Neolithic farmers).

Probably, there were multiple expansions, and also probably, we're going to have to start talking about expansions of the different I2-M223 subclades separately.

Sile
15-09-15, 09:32
genetker has changed his calculator

https://genetiker.wordpress.com/2015/09/15/k-16-admixture-analysis-of-copper-and-bronze-age-spanish-genomes/


maciano, you get a mention

Brennos
15-09-15, 15:29
genetker has changed his calculator

https://genetiker.wordpress.com/2015/09/15/k-16-admixture-analysis-of-copper-and-bronze-age-spanish-genomes/


maciano, you get a mention

I saw the link... and I keep seeing that ATP3 has 30% cca of Northern MIddle Eastern, 4% cca of Northern mongoloid, and the least percentage of Neolithic European...

And, yes, I suppose Geneticker's way of expression towards other bloggers is somewhat rude...

bicicleur
15-09-15, 16:30
I saw the link... and I keep seeing that ATP3 has 30% cca of Northern MIddle Eastern, 4% cca of Northern mongoloid, and the least percentage of Neolithic European...

And, yes, I suppose Geneticker's way of expression towards other bloggers is somewhat rude...

he even has Aurignacian (Motala & PWC) and Gravettian (Pit Grave & Afanasievo)

Maciamo
15-09-15, 16:51
I saw the link... and I keep seeing that ATP3 has 30% cca of Northern MIddle Eastern, 4% cca of Northern mongoloid, and the least percentage of Neolithic European...

And, yes, I suppose Geneticker's way of expression towards other bloggers is somewhat rude...

I really don't understand what this Genetiker guy is fretting about. The ATP3 R1b-M269 individual is clearly an outsider to Neolithic/Chalcolithic Iberia, with completely different admixtures from other samples. He can tweak his calculator, the fact remains that a combination of Northeast European (aka Gravettian), Northern Mongoloid and Northern Middle Eastern is a indubitable sign that ATP3 was a recent migrant from Eastern Europe. The only thing that remains unclear is how he got to Spain so early as there is no archaeological evidence of change of culture. But new cultures only emerge when migrations are big enough to replace the pre-existing culture. So there may have been lots of minor migrations that left virtually no discernible archaeological trace, hence our surprise.

LeBrok
15-09-15, 17:17
I really don't understand what this Genetiker guy is fretting about. The ATP3 R1b-M269 individual is clearly an outsider to Neolithic/Chalcolithic Iberia, with completely different admixtures from other samples. He can tweak his calculator, the fact remains that a combination of Northeast European (aka Gravettian), Northern Mongoloid and Northern Middle Eastern is a indubitable sign that ATP3 was a recent migrant from Eastern Europe. The only thing that remains unclear is how he got to Spain so early as there is no archaeological evidence of change of culture. But new cultures only emerge when migrations are big enough to replace the pre-existing culture. So there may have been lots of minor migrations that left virtually no discernible archaeological trace, hence our surprise.
As I mentioned in my early post here, he fits very well the first wave of conquests of horse steppe warriors. David Anthony says that first steppe warriors showed up in Balkans after 4,000 BC farming collapse.
All it took is, a band of young warriors on horses getting very advantageous and riding down there to Iberia.
They might as well be looking for the end of the world, like Alexander did, many millenia later. Anyway, as we know these Steppe guys had traveling and roaming in their blood. It is enough to check distribution of R1b around the globe to notice that.

Angela
15-09-15, 17:49
Brennos;466819]I saw the link... and I keep seeing that ATP3 has 30% cca of Northern MIddle Eastern, 4% cca of Northern mongoloid, and the least percentage of Neolithic European...

Exactly.


Brennos:And, yes, I suppose Geneticker's way of expression towards other bloggers is somewhat rude...


Ya think? :) The word that actually comes to my mind is deranged. This just isn't a good enough sample. Period.

Plus, people really believe he has isolated the "Gravettian" component, much less the "Aurignacian" component, with no samples for them at all? Haven't we learned yet how misleading it can be when people "extrapolate" these components instead of using actual ancient samples?

Athiudisc
15-09-15, 19:03
Plus, people really believe he has isolated the "Gravettian" component, much less the "Aurignacian" component, with no samples for them at all?

This. The "Gravettian-derived R1b-M269 Y haplogroup" really got me, too. :rolleyes2:

sparkey
15-09-15, 21:08
Plus, people really believe he has isolated the "Gravettian" component, much less the "Aurignacian" component, with no samples for them at all? Haven't we learned yet how misleading it can be when people "extrapolate" these components instead of using actual ancient samples?

QFT. Genetiker's components are interesting if we take away what he's calling them, but likely very misleading if we leave the labels on.

It's worth saying something good about Genetiker, though: His Y-SNP call posts are very helpful, I refer to them often.

Sile
15-09-15, 21:26
I saw the link... and I keep seeing that ATP3 has 30% cca of Northern MIddle Eastern, 4% cca of Northern mongoloid, and the least percentage of Neolithic European...

And, yes, I suppose Geneticker's way of expression towards other bloggers is somewhat rude...

rude! ...........basically if you do not support him 100% then it means you are against him mentality

Sile
15-09-15, 21:29
I really don't understand what this Genetiker guy is fretting about. The ATP3 R1b-M269 individual is clearly an outsider to Neolithic/Chalcolithic Iberia, with completely different admixtures from other samples. He can tweak his calculator, the fact remains that a combination of Northeast European (aka Gravettian), Northern Mongoloid and Northern Middle Eastern is a indubitable sign that ATP3 was a recent migrant from Eastern Europe. The only thing that remains unclear is how he got to Spain so early as there is no archaeological evidence of change of culture. But new cultures only emerge when migrations are big enough to replace the pre-existing culture. So there may have been lots of minor migrations that left virtually no discernible archaeological trace, hence our surprise.

he left the east most likely on foot as the horse according to Anthony was not domesticated until 3500BC.............he clearly did not travel alone as it would be illogical and thus he travelled with others with different markers ...............maybe he took 1 to 10 years to travel from east to west, will it matter!

Sile
15-09-15, 21:31
As I mentioned in my early post here, he fits very well the first wave of conquests of horse steppe warriors. David Anthony says that first steppe warriors showed up in Balkans after 4,000 BC farming collapse.
All it took is, a band of young warriors on horses getting very advantageous and riding down there to Iberia.
They might as well be looking for the end of the world, like Alexander did, many millenia later. Anyway, as we know these Steppe guys had traveling and roaming in their blood. It is enough to check distribution of R1b around the globe to notice that.

sorry no horse for human use at 4000BC unless you think David Anthony is wrong

LeBrok
16-09-15, 03:12
sorry no horse for human use at 4000BC unless you think David Anthony is wrong
Horse images as symbols of power[edit (https://en.wikipedia.org/w/index.php?title=Domestication_of_the_horse&action=edit&section=11)]About 4200-4000 BCE, more than 500 years before the geographic expansion evidenced by the presence of horse bones, new kinds of graves, named after a grave at Suvorovo (https://en.wikipedia.org/wiki/Suvorovo), appeared north of the Danube (https://en.wikipedia.org/wiki/Danube) delta in the coastal steppes of Ukraine near Izmail (https://en.wikipedia.org/wiki/Izmail). Suvorovo graves were similar to and probably derived from earlier funeral traditions in the steppes around the Dnieper River (https://en.wikipedia.org/wiki/Dnieper_River). Some Suvorovo graves contained polished stone mace-heads shaped like horse heads and horse tooth beads.[52] (https://en.wikipedia.org/wiki/Domestication_of_the_horse#cite_note-Dergachev1999-52) Earlier steppe graves also had contained polished stone mace-heads, some of them carved in the shape of animal heads.[53] (https://en.wikipedia.org/wiki/Domestication_of_the_horse#cite_note-Kuzmina2003-53) Settlements in the steppes contemporary with Suvorovo, such as Sredni Stog II and Dereivka (https://en.wikipedia.org/wiki/Dereivka) on the Dnieper River, contained 12%-52% horse bones.[54] (https://en.wikipedia.org/wiki/Domestication_of_the_horse#cite_note-Telegin1986-54)
When Suvorovo graves appeared in the Danube delta grasslands, horse-head maces also appeared in some of the indigenous farming towns of the Tripolye (https://en.wikipedia.org/wiki/Tripolye) and Gumelnitsa (https://en.wikipedia.org/wiki/Hamangia_culture) cultures in present-day Romania (https://en.wikipedia.org/wiki/Romania) and Moldova (https://en.wikipedia.org/wiki/Moldova), near the Suvorovo graves.[55] (https://en.wikipedia.org/wiki/Domestication_of_the_horse#cite_note-55) These agricultural cultures had not previously used polished-stone maces, and horse bones were rare or absent in their settlement sites. Probably their horse-head maces came from the Suvorovo immigrants. The Suvorovo people in turn acquired many copper ornaments from the Tripolye and Gumelnitsa towns. After this episode of contact and trade, but still during the period 4200-4000 BCE, about 600 agricultural towns in the Balkans and the lower Danube valley, some of which had been occupied for 2000 years, were abandoned.[56] (https://en.wikipedia.org/wiki/Domestication_of_the_horse#cite_note-Todorova1995-56) Copper mining ceased in the Balkan copper mines,[57] (https://en.wikipedia.org/wiki/Domestication_of_the_horse#cite_note-Pernicka1997-57) and the cultural traditions associated with the agricultural towns were terminated in the Balkans and the lower Danube valley. This collapse of "Old Europe" has been attributed to the immigration of mounted Indo-European warriors.[58] (https://en.wikipedia.org/wiki/Domestication_of_the_horse#cite_note-Gimbutas1991-58) The collapse could have been caused by intensified warfare, for which there is some evidence; and warfare could have been worsened by mounted raiding; and the horse-head maces have been interpreted as indicating the introduction of domesticated horses and riding just before the collapse.
However, mounted raiding is just one possible explanation for this complex event. Environmental deterioration, ecological degradation from millennia of farming, and the exhaustion of easily mined oxide copper ores also are cited as causal factors.[5] (https://en.wikipedia.org/wiki/Domestication_of_the_horse#cite_note-Anthony2007-5)[56] (https://en.wikipedia.org/wiki/Domestication_of_the_horse#cite_note-Todorova1995-56)
Horses interred in human graves[edit (https://en.wikipedia.org/w/index.php?title=Domestication_of_the_horse&action=edit&section=13)]The oldest possible archaeological indicator of a changed relationship between horses and humans is the appearance about 4800-4400 BCE of horse bones and carved images of horses in Chalcolithic graves of the early Khvalynsk culture (https://en.wikipedia.org/wiki/Khvalynsk_culture) and the Samara culture (https://en.wikipedia.org/wiki/Samara_culture) in the middle Volga (https://en.wikipedia.org/wiki/Volga_River) region of Russia. At the Khvalynsk cemetery near the town of Khvalynsk (https://en.wikipedia.org/wiki/Khvalynsk), 158 graves of this period were excavated. Of these, 26 graves contained parts of sacrificed domestic animals, and additional sacrifices occurred in ritual deposits on the original ground surface above the graves. Ten graves contained parts of lower horse legs; two of these also contained the bones of domesticated cattle and sheep. At least 52 domesticated sheep or goats (https://en.wikipedia.org/wiki/Goat), 23 domesticated cattle, and 11 horses were sacrificed at Khvalynsk. The inclusion of horses with cattle and sheep and the exclusion of obviously wild animals together suggest that horses were categorized symbolically with domesticated animals.[citation needed (https://en.wikipedia.org/wiki/Wikipedia:Citation_needed)]
At S’yezzhe, a contemporary cemetery of the Samara culture, parts of two horses were placed above a group of human graves. The pair of horses here was represented by the head and hooves, probably originally attached to hides. The same ritual—using the hide with the head and lower leg bones as a symbol for the whole animal—was used for many domesticated cattle and sheep sacrifices at Khvalynsk. Horse images carved from bone were placed in the above-ground ochre deposit at S’yezzhe and occurred at several other sites of the same period in the middle and lower Volga region. Together these archaeological clues suggest that horses had a symbolic importance in the Khvalynsk and Samara cultures that they had lacked earlier, and that they were associated with humans, domesticated cattle, and domesticated sheep. Thus, the earliest phase in the domestication of the horse might have begun during the period 4800-4400 BCE.[citation needed (https://en.wikipedia.org/wiki/Wikipedia:Citation_needed)]

https://en.wikipedia.org/wiki/Domestication_of_the_horse

Maciamo
16-09-15, 10:42
he left the east most likely on foot as the horse according to Anthony was not domesticated until 3500BC.............he clearly did not travel alone as it would be illogical and thus he travelled with others with different markers ...............maybe he took 1 to 10 years to travel from east to west, will it matter!

Actually David Anthony writes that the earliest evidence of horse domestication in the Pontic-Caspian steppes appears just after 4800 BCE (pp.200 and 201 in The Horse, the Wheel and Language (http://www.amazon.co.uk/gp/product/0691058873?ie=UTF8&tag=eupedia-21&linkCode=as2&camp=1634&creative=6738&creativeASIN=0691058873)). Several other sources (https://en.wikipedia.org/wiki/Domestication_of_the_horse) give a range between 4000 and 3500 BCE for horse domestication.

These are merely estimates, not hard facts. However we should understand that this is the lower limit and not the upper one. It is only based on the archaeological evidence found until now. With archaeological finds there is always the possibility that older remains will be found later that push the dates even further. In other words we can't rule out that evidence of horse domestication from, say, 5000 BCE will be found one day. This is something that I try to keep in mind for all archaeological evidence. Always be careful with age estimates as they are liable to be revised when additional data comes in.

Anyway in the case of ATP3, 3500 BCE is definitely not too early for nomadic horse riders from the Steppe. I agree with Lebrok that these might have been adventurers looking for the end of the world. After all it has been proven that R1b people from the Black Sea region (Yamna) reached the Altai (Afanasevo) as early as 3500 BCE. It is not much farther to reach northern Spain. We also have evidence of the first forays of steppe people into the Balkans happened between 4200 BCE and 3900 BCE, when cattle herders equipped with horse-drawn wagons crossed the Dniester and Danube and apparently destroyed the towns of the Gumelnita, Varna and Karanovo VI cultures.

Finalise
16-09-15, 14:59
How amazing history is! Horse riders riding from Crimea to Madrid to prove forum theories about R1b 6,000 years later.It's clear the M269*s were the Leif Ericssons, the L23*s were the Columbuses, the Z2103 the Conquistadors, and L51 the Pilgrims.

bicicleur
16-09-15, 16:19
the wheel, all of a sudden it was there +/- 3500 BC (or is this revised to 3000 BC ?)
and it spread immeadiately in Yamnaya, all over the steppe till Mongolia, in corded ware and even in Mesopotamia and central Europe

the horse, we don't know
were they just hunted? or herded? or domesticated? or ridden?
it is not clear for a long period of time
and it didn't spread in great numbers either, therefore - I guess - a domesticated horse was to expensive in maintenance costs

i'm not sure this ATP3 came on horse
he might have reached Iberia by boat too
same as you'd expect for Los Millares

bicicleur
16-09-15, 16:23
After all it has been proven that R1b people from the Black Sea region (Yamna) reached the Altai (Afanasevo) as early as 3500 BCE. It is not much farther to reach northern Spain.

wasn't the date for Afanasievo revised by Allentoft to 3000 BCE ?

nothinng in Allentoft about Suvorovo either - allthough, of course it was there

Brennos
16-09-15, 17:46
How amazing history is! Horse riders riding from Crimea to Madrid to prove forum theories about R1b 6,000 years later.It's clear the M269*s were the Leif Ericssons, the L23*s were the Columbuses, the Z2103 the Conquistadors, and L51 the Pilgrims.

Humour just doesn't work...

I don't understand a thing, and I wrote this post another time in this forum: why - I pray for an answer - when it comes to talk about R1b then all theories about its connection with IE speakers MUST be ridiculous and biased? Why R1b only must be the most maltreated haplogroup?

I'm a G2a3 man from Italy - so no conflict of interest - but I really realized that all people in many fora are against R1b carriers, in a way that I would define rich in envy and anger.

I understand that, sometimes, genetic studies aren't the field of pure science... but the field of despicable politics.

Sile
16-09-15, 20:07
Humour just doesn't work...

I don't understand a thing, and I wrote this post another time in this forum: why - I pray for an answer - when it comes to talk about R1b then all theories about its connection with IE speakers MUST be ridiculous and biased? Why R1b only must be the most maltreated haplogroup?

I'm a G2a3 man from Italy - so no conflict of interest - but I really realized that all people in many fora are against R1b carriers, in a way that I would define rich in envy and anger.

I understand that, sometimes, genetic studies aren't the field of pure science... but the field of despicable politics.

your G2a3 can be further drilled down to G2a3a ( greek aegean area ) or G2a3b ( caucasus mountains ) if you do further testing

In regards to the "Humour" ............one need to know why the move from steppe to Iberia ................which is why I think the move was in a group and took a very long time.
There was no Leif Erirsson ( I have been given a map on where I am to go ) scenario

Yetos
16-09-15, 20:31
Humour just doesn't work...

I don't understand a thing, and I wrote this post another time in this forum: why - I pray for an answer - when it comes to talk about R1b then all theories about its connection with IE speakers MUST be ridiculous and biased? Why R1b only must be the most maltreated haplogroup?

I'm a G2a3 man from Italy - so no conflict of interest - but I really realized that all people in many fora are against R1b carriers, in a way that I would define rich in envy and anger.

I understand that, sometimes, genetic studies aren't the field of pure science... but the field of despicable politics.

which part of Italy? Abrosso, Apulia?
G2a3a was detected there if remember correct.

LeBrok
17-09-15, 01:54
which part of Italy? Abrosso, Apulia?
G2a3a was detected there if remember correct.
Hey Yetos, are you going to check your Y hg soon? It would be funny if it turned Slavic-Macedonian R1a type. ;)

Maciamo
17-09-15, 07:45
the wheel, all of a sudden it was there +/- 3500 BC (or is this revised to 3000 BC ?)
and it spread immeadiately in Yamnaya, all over the steppe till Mongolia, in corded ware and even in Mesopotamia and central Europe

The wheel (and horses) enabled the true nomadic lifestyle that allowed animal herders to move constantly with their herds and all their belongings. It was very different from the nomadic way of hunter-gatherers, because H-G depended on the knowledge and richness of local environment, the seasonal migrations of wild animals, etc. With domestication and wagons, people suddenly became free of all constraints.

It may not be easy to imagine how it must have been when we look at today's world of states with borders, armies, law and police, but the world 5000 years ago was wide open for anyone who wanted to roam it. Neolithic villages were so thinly scattered that it was easy to circumvent them. It makes sense that nomadic Yamna people would have spread in all directions pretty much as far as they could. Moving south was more perilous because of diseases in warmer climes (esp. Africa) as Jared Diamond explained in Guns, Germs and Steel. But as long as they stayed roughly around the same latitude, the world is their oyster.




the horse, we don't know
were they just hunted? or herded? or domesticated? or ridden?
it is not clear for a long period of time
and it didn't spread in great numbers either, therefore - I guess - a domesticated horse was to expensive in maintenance costs

David Anthony uses bridles and mouthpieces as evidence of horse riding, and these come at least by 4000 BCE.

Why would domesticated horses be too expensive to maintain for steppe nomads ? Horses eat grass, which is plentiful in the steppe. That is their natural environment.



i'm not sure this ATP3 came on horse
he might have reached Iberia by boat too
same as you'd expect for Los Millares

I thought about it too, but there are many problems with coming to Iberia by boat.

1) In 3500 BCE galleys didn't exist yet, only smaller boats. So unless they followed the coasts all the way from the Black Sea to Spain, a journey surely as perilous as the Odyssey, it's highly improbable that they would have made it without any map or any knowledge of where they were going.

2) Add to this that small boats couldn't carry big animals like cows. If they were Steppe cattle herders, why would they suddenly leave their land bound lifestyle and migrate on boats to distant lands, without their animals ? What would they have eaten along the way ? Steppe nomads aren't fishermen and don't have knowledge of the sea.

3) We could imagine that ATP3 does not descend from Steppe nomads, but rather from some Near Eastern people. But if that is the case, the only region that would have such high frequency of Caucaso-Gedrosian (Northern Middle Eastern) in 3500 BCE would be around the Caucasus and Iran, not Anatolia and the Levant with their high EEF-like admixture + Southwest Asian and Red Sea admixtures, and certainly not Egypt. Then why would they have Mongoloid and Northeast European admixture (and mtDNA) if they came from the Middle East ?

4) El Portalon Cave is very deep inland. If they were sea travelers, why would they suddenly drop their boats and move across the Catalan mountains, the arid plains of Aragon and Castile and settle in a cave ? This is just too far fetched.

5) There is ample evidence that R1a/R1b Steppe nomads traveled quickly very long distances, to the Altai, Siberia and Mongolia to the east, and to Scandinavia to the north-west (for R1a) in just a few generations. Why would it be so hard to conceive that some early R1b nomads ended up in Iberia by the time other R1b nomads reached the Altai, even if it is 1000 years before the massive R1b invasion of Western Europe that would destroy Megalithic societies ? I suggested many years ago that the Bell Beaker culture was infiltrated progressively by small incursions of R1b people. That's what the red dots (= R1b) represent on my migration maps. It's just that these incursions may have started earlier than I thought, on a scale so small as to be undetectable by archaeological remains alone.

http://cdn.eupedia.com/images/content/early_middle_bronze_europe.png

bicicleur
17-09-15, 08:30
David Anthony uses bridles and mouthpieces as evidence of horse riding, and these come at least by 4000 BCE.

Why would domesticated horses be too expensive to maintain for steppe nomads ? Horses eat grass, which is plentiful in the steppe. That is their natural environment.



I mean in Europe.
In a short notice there where wagons everywhere.
But horses, there was only a very small elite who had them.

Sile
17-09-15, 09:04
I mean in Europe.
In a short notice there where wagons everywhere.
But horses, there was only a very small elite who had them.

where were the horses kept when the steppe was under months of snow ?

Fire Haired14
17-09-15, 09:35
@Maciamo,

ATP3 is of low coverage and Genetickers ADMIXTURE test is unreliable. Analysis of the very high coverage ATP2 showed he had no Steppe ancestry, he was a typical Neolithic European(with very high WHG). ATP3 either had very little Steppe-related ancestry or none.

bicicleur
17-09-15, 09:46
where were the horses kept when the steppe was under months of snow ?

cattle can't survive winter on the steppe without being foddered
but wild horses can clear the snow on top of the grass
according to David Anthony, that is why IE started to herd horses instead of cattle

Greying Wanderer
17-09-15, 11:20
copper workers

by sea to crete by sea to the Med. islands and eventually iberia

(others crete to cyprus to egypt etc)

hence minority presence among standard farmers

imo

Brennos
17-09-15, 12:36
@Maciamo,

ATP3 is of low coverage and Genetickers ADMIXTURE test is unreliable. Analysis of the very high coverage ATP2 showed he had no Steppe ancestry, he was a typical Neolithic European(with very high WHG). ATP3 either had very little Steppe-related ancestry or none.


So, why its admixture is unreliable, but its attribution to haplogroup R-M269 is reliable?

Richard Rocca on Anthrogenica noticed that in the site where ATP3 is buried there is a wrist guard and arrow points.


And, the last thing, probably, ATP2 and ATP3 weren't connected to each other at all: many years were spent between the two individuals.

Brennos
17-09-15, 12:38
your G2a3 can be further drilled down to G2a3a ( greek aegean area ) or G2a3b ( caucasus mountains ) if you do further testing

In regards to the "Humour" ............one need to know why the move from steppe to Iberia ................which is why I think the move was in a group and took a very long time.
There was no Leif Erirsson ( I have been given a map on where I am to go ) scenario

Thanks for suggestion Sile, but, frankly, I'm not interested at all about my haplogroup: its origins are somewhat understood now. I'm much more interested in R1b, the greatest mystery in European history!

Brennos
17-09-15, 12:39
which part of Italy? Abrosso, Apulia?
G2a3a was detected there if remember correct.

From Northern Italy, Bergamo.

MOESAN
17-09-15, 18:47
[QUOTE=bicicleur;466547]this is what I have



Spain
Els Trocs [Troc3]
M
5178-5066 BC
R1b1c
M415+, M343+, [L754 equivalent: L774/PF6245/YSC277+, PF1144+, V88 eqivalent: PF6376+]
M478-, PF6399-, L265-, L150-, M269-, V35-, V69-
pre-T2c1d2
Haak 2015; personal comm Sergey Malyshev, review of Y-DNA raw data


[/QUOTE )


SO it is the same, and he was Y R-V88; thanks for the confirmation; it does not prove nor disprove more at this stage conncerning other M269 derived in Europe

MOESAN
17-09-15, 19:29
I don't know how some people can still view L23->L51 at the heart of the IE expansions even after all the evidence. R1a's connection to IE speakers is undisputed after Sintasha findings, modern high R1a frequencies in South Asia and their link to Corded Ware. L23->Z2103 is found in steppe at high frequencies and it is prevalent in Western Asia, Balkans, Eastern Europe where IE languages are spoken.L51 is nowhere to be found around the steppe, and the most likely scenario is that L23's homeland is around Eastern Anatolia, with the northern branch of Z2103 being the Maykops/Steppe people, and the western branch of L51 being the farming branch that travels through the Danube to western Europe. El Portalon just confirms this.

I 'm not persuaded Y-R1a is the I-Eans basis; rather an acculturated group of ethnies which gave rise to the satem group (where I would put Corded). For the origin of Y-R1b L23 you could be right, even if the Maykop episode is still to be better understood (sense of moves: culture moves can be opposite to demic moves in osmosis: not to forget). The differences between Yamnaya and Catacombs, even if far from being total, could be due to a strong presence of Y-R1b-L23 among these last ones, with perhaps also Y-G2a. They could have been a remained party of other L23 I-Eans already routing West and North. I avow it's pure guess. Some archeologists think Catacombs are rather indo-aryan concerning artefacts; but artefacts and modes can change with time, quicker than language, itself changing faster than whole population genomes. Other archeologist Konitsev) thinks Sintashta were culturally close to Indo-Iranians culture.
If El Trocs3 is R-V88, he don't prove nothing about other R-M269 derived haplos. Concerning L51, he is present too in Northern Europe, South Sweden and I keep in mind the allover diversity of Y-R1b was said to be greater in East Nortern Europe than in South-West Europe, the Basques being the poorest (Irish not far); perhaps newer studies could disprove this? THat does not discard a Neolithic wave along the Danube but here we have to imagine a NEW>wave and to FIND Y-R1b DNA among LBK or successors: let's wait but it seems very uncertain. I keep in my sleeve the possibility of a Y-R1b wave or demic accumulation by maritime ways at the maritime Megalithics period (different neolithical people, later) and just after but... very hypothetic too, fragile! it would imply a rapid introgression into inlands (Central France?) before demic explosion leaving Basques ancestors aside for a while???. or a mix of lands and see ways?
Sorry if I'm not as sure of mine as some forumers.
Good afternoon

MOESAN
17-09-15, 19:33
@Maciamo,

ATP3 is of low coverage and Genetickers ADMIXTURE test is unreliable. Analysis of the very high coverage ATP2 showed he had no Steppe ancestry, he was a typical Neolithic European(with very high WHG). ATP3 either had very little Steppe-related ancestry or none.

the new Genetiker analysis is surprising concerning poolings: I admit I've some doubts about his objectivity and poolings accuracy - here under:

ATP2 ATP3 ATP7 ATP9 ATP12 ATP16 ATP17 ATP20
Neolithic European 80.38 49.49 88.17 67.83 82.82 90.82 99.53 54.34
Gravettian 10.29 12.62 11.82 28.38 0.00 2.30 0.00 0.00
Aurignacian 8.42 3.83 0.00 2.53 17.17 6.36 0.45 10.46
Northern Mideastern 0.00 30.39 0.00 0.00 0.00 0.00 0.00 0.00
Veddoid-Caucasoid 0.00 0.00 0.00 0.14 0.00 0.00 0.00 28.91
Amerindian 0.06 0.00 0.00 0.07 0.00 0.00 0.00 6.28
Northern Mongoloid 0.84 3.66 0.00 0.00 0.00 0.51 0.00 0.00
Australoid 0.00 0.00 0.00 1.04 0.00 0.00 0.00 0.00
Southern Mideastern 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
Eskimo 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
Bushman 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
Taiwanese aborigine 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
Western Negroid 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
Southern Mongoloid 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
Eastern Negroid 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
Pygmy 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00

​different from his first analysis

MOESAN
17-09-15, 19:38
@Maciamo,

ATP3 is of low coverage and Genetickers ADMIXTURE test is unreliable. Analysis of the very high coverage ATP2 showed he had no Steppe ancestry, he was a typical Neolithic European(with very high WHG). ATP3 either had very little Steppe-related ancestry or none.

Genetiker made a new analysis with surprising poolings based upon ??? It have some doubts about his objectivity, but who knows?
ATP2 ATP3 ATP7 ATP9 ATP12 ATP16 ATP17 ATP20
Neolithic European 80.38 49.49 88.17 67.83 82.82 90.82 99.53 54.34
Gravettian 10.29 12.62 11.82 28.38 0.00 2.30 0.00 0.00
Aurignacian 8.42 3.83 0.00 2.53 17.17 6.36 0.45 10.46
Northern Mideastern 0.00 30.39 0.00 0.00 0.00 0.00 0.00 0.00
Veddoid-Caucasoid 0.00 0.00 0.00 0.14 0.00 0.00 0.00 28.91
Amerindian 0.06 0.00 0.00 0.07 0.00 0.00 0.00 6.28
Northern Mongoloid 0.84 3.66 0.00 0.00 0.00 0.51 0.00 0.00
Australoid 0.00 0.00 0.00 1.04 0.00 0.00 0.00 0.00
Southern Mideastern 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
Eskimo 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
Bushman 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
Taiwanese aborigine 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
Western Negroid 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
Southern Mongoloid 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
Eastern Negroid 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
Pygmy 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00

Angela
17-09-15, 21:11
I 'm not persuaded Y-R1a is the I-Eans basis; rather an acculturated group of ethnies which gave rise to the satem group (where I would put Corded). For the origin of Y-R1b L23 you could be right, even if the Maykop episode is still to be better understood (sense of moves: culture moves can be opposite to demic moves in osmosis: not to forget). The differences between Yamnaya and Catacombs, even if far from being total, could be due to a strong presence of Y-R1b-L23 among these last ones, with perhaps also Y-G2a. They could have been a remained party of other L23 I-Eans already routing West and North. I avow it's pure guess. Some archeologists think Catacombs are rather indo-aryan concerning artefacts; but artefacts and modes can change with time, quicker than language, itself changing faster than whole population genomes. Other archeologist Konitsev) thinks Sintashta were culturally close to Indo-Iranians culture.
If El Trocs3 is R-V88, he don't prove nothing about other R-M269 derived haplos. Concerning L51, he is present too in Northern Europe, South Sweden and I keep in mind the allover diversity of Y-R1b was said to be greater in East Nortern Europe than in South-West Europe, the Basques being the poorest (Irish not far); perhaps newer studies could disprove this? THat does not discard a Neolithic wave along the Danube but here we have to imagine a NEW>wave and to FIND Y-R1b DNA among LBK or successors: let's wait but it seems very uncertain. I keep in my sleeve the possibility of a Y-R1b wave or demic accumulation by maritime ways at the maritime Megalithics period (different neolithical people, later) and just after but... very hypothetic too, fragile! it would imply a rapid introgression into inlands (Central France?) before demic explosion leaving Basques ancestors aside for a while???. or a mix of lands and see ways?
Sorry if I'm not as sure of mine as some forumers.
Good afternoon

This is generally how I see it as well, and I have many of the same questions. I think we have to remember that Haak et al were very careful to state they were only dealing with one part of the spread of the Indo-European languages into Europe.

Maciamo
18-09-15, 07:59
where were the horses kept when the steppe was under months of snow ?

Horses can dig in the snow with their hoofs to clear up the grass. Otherwise how would they have survived in the wild before domestication ?

Fire Haired14
18-09-15, 08:54
So, why its admixture is unreliable, but its attribution to haplogroup R-M269 is reliable?

Richard Rocca on Anthrogenica noticed that in the site where ATP3 is buried there is a wrist guard and arrow points.


And, the last thing, probably, ATP2 and ATP3 weren't connected to each other at all: many years were spent between the two individuals.

Y SNPs are straightforward. Other have confirmed Geneticker's results. ADMIXTURE results can vary depending on how experienced the maker of an ADMIXTURE test is. Also, ATP3 is of low coverage so his ADMIXTURE results won't be accurate. Other analysis of ATP3 shows him as a typical Middle Neolithic guy with maybe some ANE.

We've seen genetic continuation from Hungary-Spain ranging 5500-3000 BC. Almost nothing changed in that region for 2500 years. The only change was 20-30% added WHG ancestry. Yes, ATP3 and ATP2 are separated by many hundreds of years, but because of what we've seen in ancient DNA before it wuld be very strange if ATP3 was anything but a typical Middle Neolithic European.

Arame
18-09-15, 10:08
Btw. Why the more earlier than expected apparition of R1b-L51 in West Europe is viewed as a problem for his link to IE.
Wasn't it expected something like this based on the age estimates of Celtic, Italic and Germanic by David Anthony?
Germanic 3300BC
Italic 3000BC
Celtic 3000BC

https://en.wikipedia.org/wiki/Indo-European_languages#Classification
http://2.bp.blogspot.com/-Et6SS_bTFtc/VM740osEIeI/AAAAAAAAJ5I/3JmZBNHvNFU/s1600/annurev-linguist-030514-124812.f2.jpeg

Fire Haired14
18-09-15, 13:55
Btw. Why the more earlier than expected apparition of R1b-L51 in West Europe is viewed as a problem for his link to IE.
Wasn't it expected something like this based on the age estimates of Celtic, Italic and Germanic by David Anthony?
Germanic 3300BC
Italic 3000BC
Celtic 3000BC

https://en.wikipedia.org/wiki/Indo-European_languages#Classification
http://2.bp.blogspot.com/-Et6SS_bTFtc/VM740osEIeI/AAAAAAAAJ5I/3JmZBNHvNFU/s1600/annurev-linguist-030514-124812.f2.jpeg

The theory is that IE languages were brought to West Europe with heavily Steppe-admixed people in 2800 BC who had Y DNA R1b-L151. R1b-L151 and IE languages in West Europe in 3500 BC would completly prove this theory incorrect.

Anyways, Germanic languages expanded in the early historic period(~0-700 AD) and most Celtic/Italic languages might have expanded in the Early Iron age(1000-500 BC). The idea they expanded around 3000 BC is insane. Those languages didn't expand the moment IEs arrived.

Germanic evolved in Scandinavia and Celtic/Italic evolved in Germany/Hungary/Austria area for 2,000 years before they expanded.

Brennos
18-09-15, 14:40
The theory is that IE languages were brought to West Europe with heavily Steppe-admixed people in 2800 BC who had Y DNA R1b-L151. R1b-L151 and IE languages in West Europe in 3500 BC would completly prove this theory incorrect.

Anyways, Germanic languages expanded in the early historic period(~0-700 AD) and most Celtic/Italic languages might have expanded in the Early Iron age(1000-500 BC). The idea they expanded around 3000 BC is insane. Those languages didn't expand the moment IEs arrived.

Germanic evolved in Scandinavia and Celtic/Italic evolved in Germany/Hungary/Austria area for 2,000 years before they expanded.

Do you think that ATP3 could be R-L151?

Brennos
18-09-15, 14:42
But, frankly, the new analysis by Genetiker of that ATP3 individual are very similar to the first analysis done: he seems to be East-shifted.

Sennevini
18-09-15, 15:22
Btw. Why the more earlier than expected apparition of R1b-L51 in West Europe is viewed as a problem for his link to IE.
Wasn't it expected something like this based on the age estimates of Celtic, Italic and Germanic by David Anthony?
Germanic 3300BC
Italic 3000BC
Celtic 3000BC

https://en.wikipedia.org/wiki/Indo-European_languages#Classification
http://2.bp.blogspot.com/-Et6SS_bTFtc/VM740osEIeI/AAAAAAAAJ5I/3JmZBNHvNFU/s1600/annurev-linguist-030514-124812.f2.jpeg

For expansion it's too early,
but for the split of dialects from the other IE dialects, it is possible.

Arame
18-09-15, 16:15
Fire Haired

I see what You say. I don't mean an expansion of Germanic, I mean the split. For the split some space is needed. A relatively isolated place is needed and big distance from neighbouring other IEs to exclude any convergence.

I think the big problem for L51>L11 to be linked to IE would be to find an aDNA without any ANE. That will put end to that theory. But until now there is no such aDNA. Even this dubious R1b-M269 seems to have some ANE, and he is not even L23+ or L51+.

MOESAN
20-10-15, 22:40
I shall come on this topic at the week end;
as the topic is about Basques, ancient or current ones, I put here some thoughts of Eurogenes-Davidski (Polako?)

Friday, October 16, 2015

Basques are not simply a fusion of Iberian hunter-gatherers and early farmers (http://eurogenes.blogspot.fr/2015/10/basques-are-not-simply-fusion-of.html)

I thought I'd revisit the issue of Basque origins with my new Principal Component Analysis (PCA) of West Eurasia. The useful thing about this PCA is that it gets around two problems that routinely affect PCA featuring ancient samples: projection bias, otherwise known as shrinkage, and exaggerated outcomes for individuals with high counts of homozygous genotypes.
file:///C:/Users/Joachim/AppData/Local/Temp/msohtmlclip1/01/clip_image002.jpg (https://drive.google.com/file/d/0B9o3EYTdM8lQLVlFbmI5RTYzNWM/view?usp=sharing)

A couple of recent papers argued that Basques were the direct descendants of local hunter-gatherers and early Neolithic farmers who arrived in Iberia from the eastern Mediterranean. This is probably correct for the most part, but it doesn't tell the whole story.

On the PCA above, Basques are quite distinct from Early Neolithic, Middle Neolithic and Copper Age Iberians (marked Iberia_EN, Iberia_MN and Iberia_CA, respectively), because they are significantly more eastern. In fact, they cluster with the only Bronze Age Iberian on the plot (Iberia_BA), which is the same individual that I found to harbor steppe-related ancestry (see here (http://eurogenes.blogspot.com.au/2015/09/steppe-related-admixture-in-bronze-age.html)).

Thus, the story told by the PCA is that Basques are the progeny of Bronze Age Iberians, who, unlike their Copper Age predecessors, experienced a pulse of steppe-related admixture from the east.

Formal statistics back this up. For instance, here's a quote from the recently revised Mathieson et al. preprint (http://eurogenes.blogspot.com.au/2015/10/eight-thousand-years-of-natural.html):
However, the statistic f4(Basque, Iberia_Chalcolithic; Yamnaya_Samara,Chimp)=0.00168 is significantly positive (Z=8.1), as is the statistic f4(Spanish, Iberia_Chalcolithic; Yamnaya_Samara, Chimp)= 0.00092 (Z=4.6). This indicates that steppe ancestry occurs in present-day southwestern European populations, and that even the Basques cannot be considered as mixtures of early farmers and hunter-gatherers without it (4).

The key question now is who brought the steppe-related ancestry to Basque country. Were they Indo-Europeans or speakers of Proto-Basque? Also, did they actually come from the steppe, or somewhere nearby, like the Carpathian Basin?

The reason I mention the Carpathian Basin is because, as per the PCA, Basques more or less cluster between Copper Age Iberians and some of the Bronze Age Hungarians (marked Hungary_BA). But this is just one possibility, and I'm not sure at this stage how plausible it looks with, say, formal statistics.

In this analysis I used samples from the Allentoft et al. (http://www.nature.com/nature/journal/v522/n7555/full/nature14507.html), Gunther et al. (http://www.pnas.org/content/early/2015/09/02/1509851112.abstract), Haak et al. (http://www.nature.com/nature/journal/vaop/ncurrent/full/nature14317.html) and Lazaridis et al. (http://www.nature.com/nature/journal/v513/n7518/full/nature13673.html) datasets, all of which are publicly available. The latter two are found at the Reich Lab site here (http://genetics.med.harvard.edu/reichlab/Reich_Lab/Datasets.html). If you're confused by some of the acronyms in the PCA key, see here (https://drive.google.com/file/d/0B9o3EYTdM8lQT0MzSzVwR0pNenc/view?usp=sharing).
Posted by Davidski (https://www.blogger.com/profile/04637918905430604850)








ATP2 ATP3 ATP7 ATP9 ATP12 ATP16 ATP17 ATP20
Neolithic European 80.38 49.49 88.17 67.83 82.82 90.82 99.53 54.34
Gravettian 10.29 12.62 11.82 28.38 0.00 2.30 0.00 0.00
Aurignacian 8.42 3.83 0.00 2.53 17.17 6.36 0.45 10.46
Northern Mideastern 0.00 30.39 0.00 0.00 0.00 0.00 0.00 0.00
Veddoid-Caucasoid 0.00 0.00 0.00 0.14 0.00 0.00 0.00 28.91
Amerindian 0.06 0.00 0.00 0.07 0.00 0.00 0.00 6.28
Northern Mongoloid 0.84 3.66 0.00 0.00 0.00 0.51 0.00 0.00
Australoid 0.00 0.00 0.00 1.04 0.00 0.00 0.00 0.00
Southern Mideastern 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
Eskimo 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
Bushman 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
Taiwanese aborigine 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
Western Negroid 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
Southern Mongoloid 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
Eastern Negroid 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
Pygmy 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00

MOESAN
20-10-15, 22:45
I tried to copy/paste a post of Eurogenes (Polako?) concerning the drift of today Basques towards something "east": HG Samara or BA Yamnaya?
all the way the text is available on his blog - I shall say ma thought this week end -
good challenges!

MOESAN
22-10-15, 18:27
Friday, October 16, 2015

Basques are not simply a fusion of Iberian hunter-gatherers and early farmers (http://eurogenes.blogspot.fr/2015/10/basques-are-not-simply-fusion-of.html)

I thought I'd revisit the issue of Basque origins with my new Principal Component Analysis (PCA) of West Eurasia. The useful thing about this PCA is that it gets around two problems that routinely affect PCA featuring ancient samples: projection bias, otherwise known as shrinkage, and exaggerated outcomes for individuals with high counts of homozygous genotypes.
image erased here
A couple of recent papers argued that Basques were the direct descendants of local hunter-gatherers and early Neolithic farmers who arrived in Iberia from the eastern Mediterranean. This is probably correct for the most part, but it doesn't tell the whole story.

On the PCA above, Basques are quite distinct from Early Neolithic, Middle Neolithic and Copper Age Iberians (marked Iberia_EN, Iberia_MN and Iberia_CA, respectively), because they are significantly more eastern. In fact, they cluster with the only Bronze Age Iberian on the plot (Iberia_BA), which is the same individual that I found to harbor steppe-related ancestry (see here (http://eurogenes.blogspot.com.au/2015/09/steppe-related-admixture-in-bronze-age.html)).

Thus, the story told by the PCA is that Basques are the progeny of Bronze Age Iberians, who, unlike their Copper Age predecessors, experienced a pulse of steppe-related admixture from the east.

Formal statistics back this up. For instance, here's a quote from the recently revised Mathieson et al. preprint (http://eurogenes.blogspot.com.au/2015/10/eight-thousand-years-of-natural.html):
However, the statistic f4(Basque, Iberia_Chalcolithic; Yamnaya_Samara,Chimp)=0.00168 is significantly positive (Z=8.1), as is the statistic f4(Spanish, Iberia_Chalcolithic; Yamnaya_Samara, Chimp)= 0.00092 (Z=4.6). This indicates that steppe ancestry occurs in present-day southwestern European populations, and that even the Basques cannot be considered as mixtures of early farmers and hunter-gatherers without it (4).

The key question now is who brought the steppe-related ancestry to Basque country. Were they Indo-Europeans or speakers of Proto-Basque? Also, did they actually come from the steppe, or somewhere nearby, like the Carpathian Basin?

The reason I mention the Carpathian Basin is because, as per the PCA, Basques more or less cluster between Copper Age Iberians and some of the Bronze Age Hungarians (marked Hungary_BA). But this is just one possibility, and I'm not sure at this stage how plausible it looks with, say, formal statistics.

In this analysis I used samples from the Allentoft et al. (http://www.nature.com/nature/journal/v522/n7555/full/nature14507.html), Gunther et al. (http://www.pnas.org/content/early/2015/09/02/1509851112.abstract), Haak et al. (http://www.nature.com/nature/journal/vaop/ncurrent/full/nature14317.html) and Lazaridis et al. (http://www.nature.com/nature/journal/v513/n7518/full/nature13673.html) datasets, all of which are publicly available. The latter two are found at the Reich Lab site here (http://genetics.med.harvard.edu/reichlab/Reich_Lab/Datasets.html). If you're confused by some of the acronyms in the PCA key, see here (https://drive.google.com/file/d/0B9o3EYTdM8lQT0MzSzVwR0pNenc/view?usp=sharing).
Posted by Davidski (https://www.blogger.com/profile/04637918905430604850)

MOESAN
22-10-15, 18:27
file:///C:/Users/Joachim/AppData/Local/Temp/msohtmlclip1/01/clip_image002.jpg (https://drive.google.com/file/d/0B9o3EYTdM8lQLVlFbmI5RTYzNWM/view?usp=sharing)

MOESAN
22-10-15, 19:01
I know plottings are not maybe not sufficiant to appreciate distances and trends; I see Basques shifted for the most towards Hgs when compared to Sardinians and Neolithic populations (and the Chalcolithoc ones of Iberia): something more "North" more "West"; some could say their HG's direction is almost more Scandinavianlike than Iberianlike?
In fact the slight more proximity they show with Steppic people seems more the result of ancient Samara HGs and even Karelia having a strong common ancient HGs heritage.
It remains they have some 'gedrosia' and share something with North-East Europe people (mtDNA roots of some haplo's); some ratios as 'gedrosia'/'caucasus', 'basque'/'sardinian' in some poolings show strong enough relations with the Isles and West Scandinavia, a bit less with Finland; by the way here again, Lithuanians and Slavs are opposed to Basques and other Northern people, as if they were really composed of a component which was avoided by some East-West moves, if not by all of these moves, of course!
so the I-Ean link seems very weak in Basques, they have little of southern part of the 'teal' or 'central-asian' component if any, I think.