The genetic structure of the world’s first farmers

That model had high standard errors and is therefore not a realistic model for Anatolia_N. Anatolia_N doesn't fit well as a mixture of other ancient genomes. We need more ancient genomes to learn who the ancestors of Anatolia_N were. It probably has some Iran_Neolithic ancestry but not a lot, definitely not 34%. Anatolia_N is also definitely not 27% WHG. Anatolia_N appears to be a brother to Levant_N.



Iran Chl is a mixture of CHG(or Iran Neolithic. Both were similar) and Levant_Neolithic. Armenia_EBA is a mixture of CHG, Levant_Neolithic(or Anatolila_Neolithic. Both were similar), and EHG.

It is not even clear if EHG or WHG. Armenian EBA does not shows any more significant EHG(or WHG) admixture than Iranian or Anatolian Calcolthic. In fact Armenian Calcolthic had twice as much of it already. In fact the "EHG" in Armenian EBA looks identical to that of CHG. With other words Armenian EBA looks like CHG with Anatolian_Neo admixture. Or alterntively and better fitting Armenia EBA can be modeled as Armenia_Chl + Iran_Chl

With other words the "EHG/WHG" admixture was present there already during the mesolithic and in much higher frequency even already during the calcolthic.

 
Everything actually makes very good sense though. We see EHG start to pop up in Iran and the Zagros around the chalcolithic, which is when we started to see the Teal increase in Steppe samples. Not surprised to see R1b in bronze age Armenia as it comes with some EHG and is the perfect spot and time for the arrival of the Anatolian languages, keeping in mind that neolithic Armenia was all L2(?) Kura axes however is highly unlikely to be IE. Probably Hurrian or Caucasian or ancestral to those languages. Also as we move to the late Bronze age in Armenia we see a shift towards the steppe, which is consistent with ever increasing steppe influence as we move through the bronze age.

:rolleyes:

No, Iran_CHL does not have any EHG. CHG which is mesolithic does however have, Armenian EBA level, "EHG like" admixture. Armenian EBA looks pretty much like Armenian CHL + Iran CHL. Armenian Calcolthic has significantly higher frequency of "EHG " like ancestry (note they do not differentiate EHG-WHG in the graph it seems) than Armenian EBA. So whatever happened in the Armenian EBA it actually decreased the "EHG" admixture.



We'll have to see what the P* in neolithic Iran is. If it's R1b that could be a surprise to some, but it shouldn't be. R2 at this point would make more sense.

Suprise :rolleyes:

And why do you think R2 at this point makes more sense? I doubt anyone would have thought of R2 if not a dubious Blogger brought this theory up.
 
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And actually, the admixture in ANI might make linguistic sense. Iranian actually appears to be a bastardized version of Indic that was passed down through oral tradition more so than written. So Indic being associated perhaps with earlier (less admixed?) steppe makes sense.

Alone through this statement I get the impression that you don't have much clue about the whole subject. If you actually knew a little bit of genetics, linguistics and archeology such you wouldn't have written this comment. This statement doesn't make linguistically, let alone genetically sense.

The extend of phantasy in some of your theories rival the phantasy found in Gogas.
 
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No surprise to see in Armenia the same clade that appear among yamnayans two hundred years after? In a culture (Kura-Araxes) related to Maykop? And knowing that what we know by sure now is that there was a migration northwards? By simple chance the presence of R1b in Yamnaya is debt to such migration instead of EHG going south: because the demographical difference is high enough and the expansive nature of the neolithic are giving more numbers.

Kurgans appear in Anatolia around 2000 BC, the time for Anatolian languages... so to late for that.

Another (big) problem doing this R1b clade being a paleolithic migrant is that its TMRCA is after Armenia was already populated by Neolithics...
People who base their theories on things they read on blogger websites are not usualy known for common sense.

It's always the same game, the blogger doesn't have the courage to defend his ideas on foreign ground and sends his deputies to spred his word.

And no there isn't any "Basal" R1b nor R1a around Samara, they don't seem to know what basal means. No m343 or l62 found. There are many R1 lineages but all slightly downstream.
 
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From Iosif Lazardis:

"It's great to see the data already being analyzed and I hope it will be useful in your analyses!

I just wanted to leave a brief comment that the model of Steppe_EMBA as a mixture of EHG+CHG is rejected (Table S7.11), while that of EHG+Iran_ChL is not. Note that in Table S7.11 we are modeling Steppe_EMBA and the references with respect to 13 outgroup populations (the set O9ALNW), not all of which are included in the TreeMix graph.

It is possible for some models to succeed with a particular set of outgroups (both EHG+CHG and EHG+Iran_ChL are feasible with only the O9 set of outgroups; Table S7.10), but for some of them to be rejected when additional outgroups are introduced (Table S7.11). As we mention further down, that doesn't mean there is no CHG-related ancestry in Steppe_EMBA as we can model it as a 3-way mixture involving CHG as one of the sources. What it does mean, however, is that CHG+EHG cannot be the only sources, as this model is rejected (Table S7.11). A further test of our overall model is that when we withhold Iran_ChL as a source, and infer mixture proportions by intersecting the EHG->Steppe_EMBA and Levant_N+Levant_BA clines (p. 134), we get fairly reasonable agreement (mixture proportions).

We try to be cautious in our interpretation of the admixture models, because of three factors: (i) we don't know the geographical extent of populations like "CHG" or "Iran_ChL" so admixture from Iran_ChL does not imply admixture from geographical Iran or CHG from the geographical Caucasus, (ii) we do not have samples from many places and it's very likely that slightly different mixtures than the sampled populations existed elsewhere, (iii) it is possible that the actual history of admixture may be more complex than the simplest parsimonious models identified by the analysis.

Overall, our admixture analysis rejects several possible models (such as EHG+CHG) and thus puts constraints on what may have happened, and also proposes some models that are more resilient to rejection (such as EHG+Iran_ChL+CHG). But, by no means should these be regarded as the final word or unique solutions, but rather as one possible way that the data can be modeled."

Nice of him to clarify for people who haven't read the Supplement carefully.

From RK:
"
Just a quick point: even if southern admixture did arrive via the Caucasus, there is little reason to assume that it was pure CHG, free from Iran_N ancestry by the time it entered on the steppe. In the timeframe between the Khvalynsk and the Yamnaya where southern ancestry increased a great deal, the Caucasus was already agricultural, and for quite some time. Even in the pre-Khvalynsk period this was already the case. Tying in cultural packages with genetics, the demographic impact of Iran_N ancestry in India and Iran would almost definitely be repeated in the Caucasus. If southern ancestry in Yamnaya was limited to Kotias hunter-gatherers exclusively, then almost pure CHG Hunter-Gatherers must have existed hidden somewhere between the agricultural Caucasus and the emerging pastoral Yamnaya for thousands of years, and then on top of that somehow gene flow was limited to the HG groups, which I find very unlikely."

That seems sensible to me.
 
From Iosif Lazardis:

"It's great to see the data already being analyzed and I hope it will be useful in your analyses!

I just wanted to leave a brief comment that the model of Steppe_EMBA as a mixture of EHG+CHG is rejected (Table S7.11), while that of EHG+Iran_ChL is not. Note that in Table S7.11 we are modeling Steppe_EMBA and the references with respect to 13 outgroup populations (the set O9ALNW), not all of which are included in the TreeMix graph.

It is possible for some models to succeed with a particular set of outgroups (both EHG+CHG and EHG+Iran_ChL are feasible with only the O9 set of outgroups; Table S7.10), but for some of them to be rejected when additional outgroups are introduced (Table S7.11). As we mention further down, that doesn't mean there is no CHG-related ancestry in Steppe_EMBA as we can model it as a 3-way mixture involving CHG as one of the sources. What it does mean, however, is that CHG+EHG cannot be the only sources, as this model is rejected (Table S7.11). A further test of our overall model is that when we withhold Iran_ChL as a source, and infer mixture proportions by intersecting the EHG->Steppe_EMBA and Levant_N+Levant_BA clines (p. 134), we get fairly reasonable agreement (mixture proportions).

We try to be cautious in our interpretation of the admixture models, because of three factors: (i) we don't know the geographical extent of populations like "CHG" or "Iran_ChL" so admixture from Iran_ChL does not imply admixture from geographical Iran or CHG from the geographical Caucasus, (ii) we do not have samples from many places and it's very likely that slightly different mixtures than the sampled populations existed elsewhere, (iii) it is possible that the actual history of admixture may be more complex than the simplest parsimonious models identified by the analysis.

Overall, our admixture analysis rejects several possible models (such as EHG+CHG) and thus puts constraints on what may have happened, and also proposes some models that are more resilient to rejection (such as EHG+Iran_ChL+CHG). But, by no means should these be regarded as the final word or unique solutions, but rather as one possible way that the data can be modeled."

Nice of him to clarify for people who haven't read the Supplement carefully.

From RK:
"
Just a quick point: even if southern admixture did arrive via the Caucasus, there is little reason to assume that it was pure CHG, free from Iran_N ancestry by the time it entered on the steppe. In the timeframe between the Khvalynsk and the Yamnaya where southern ancestry increased a great deal, the Caucasus was already agricultural, and for quite some time. Even in the pre-Khvalynsk period this was already the case. Tying in cultural packages with genetics, the demographic impact of Iran_N ancestry in India and Iran would almost definitely be repeated in the Caucasus. If southern ancestry in Yamnaya was limited to Kotias hunter-gatherers exclusively, then almost pure CHG Hunter-Gatherers must have existed hidden somewhere between the agricultural Caucasus and the emerging pastoral Yamnaya for thousands of years, and then on top of that somehow gene flow was limited to the HG groups, which I find very unlikely."

That seems sensible to me.

Would love to give that a thumps up but can't.

This all makes allot of sentence. Remember when the CHG samples were modeled using blogger calculators? CHG turned out as roughly ~30% "Gedrosia" and ~50% Caucasus .

HOWEVER the Yamna samples modeled with the same calculator had ~27% "Gedrosia" but only ~3% Caucasus. Where was all the "Caucasus" gone? Obviously this didn't fit very much and everyone was expecting a more Gedrosia like group to be the source for the Teal admixture.

Now we have Iran_Neo/Chl samples and those from the wording of the study and where it is found and in whom it peaks (Balochi), indicate that this is the more Gedrosia like source we were searching for. Or at least Iran_Chl makes more sense than CHG.

Now someone post that one Eurogenes, where some people don't seem to have enough archeological and historic understanding and still believe mesolithic CHG+EHG is the best model for Bronze Age Yamna.
 
I already said this in the past various times, I do believe also that Basal Eurasian is connected to G, makes sense if you look at the yDNA tree.

Basal Eurasian is the first branch to split up from the main Eurasian body.

So is G from HIJK. Basal Eurasian => G was found in Iran_Neo too. And I think these ar ethe guys who brought Basal Eurasian and they must have evolved somewhere on the southern coast of Iran.

I still have my doubts that E1b1b or even E in general came from Africa, if that was the case we would see stronger signal between Sub Saharan Africans and Natufians than SSA to other Eurasians however SSA shares as much with Natufians as it shares with other Eurasians. This indicates that it can't have come from Africa, while on the opposite hand we do have Eurasian signals already in Mota and it is around ~4%.

E1b carriers looks heavily admixed with Eurasians, you only need to see their mtDNA haplogroups. If we would expect strong signals of shared autosomal DNA, we would expect E1b carriers conserving their original mtDNA but this is not the case. They are clearly "hybrids".
 
R1b-M269 first pops up in Western Europe 4600 years ago. It was absent in EEF. No other Neolithic people came to Western Europe besides EEF, then in the Bronze age Steppe people with R1b came. This is all old news.
That 's true until the next discoveries. The R1b-L23 must have been somewhere between Europe and Near East, 6500 years ago.
We try to understand the all story with less than 1% of the words.
 
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PCA chart (ancient pops):

https://twitter.com/iosif_lazaridis

wykres_PCA.png


Modern pops highlighted:

nature13673-f2.jpg
 
Would love to give that a thumps up but can't.

This all makes allot of sentence. Remember when the CHG samples were modeled using blogger calculators? CHG turned out as roughly ~30% "Gedrosia" and ~50% Caucasus .

HOWEVER the Yamna samples modeled with the same calculator had ~27% "Gedrosia" but only ~3% Caucasus. Where was all the "Caucasus" gone? Obviously this didn't fit very much and everyone was expecting a more Gedrosia like group to be the source for the Teal admixture.

Now we have Iran_Neo/Chl samples and those from the wording of the study and where it is found and in whom it peaks (Balochi), indicate that this is the more Gedrosia like source we were searching for. Or at least Iran_Chl makes more sense than CHG.

Now someone post that one Eurogenes, where some people don't seem to have enough archeological and historic understanding and still believe mesolithic CHG+EHG is the best model for Bronze Age Yamna.

I'm not clear about where you disagree with Lazaridis. He is saying CHG + EHG is rejected, while EHG + Iran Chalcolithic is not. He's also implying, I think, that they don't yet have the sample from the specific population which went north. If they did, the fits would obviously be better. During the Chalcolithic there were probably a number of populations in the northern Near East with slightly different mixes of ancestries. The one that did go north may have picked up more Levant or Anatolia EEF, but be relatively close to Iran Chalcolithic.

At any rate it's pretty clear, in my opinion, that Yamnaya is not a mix of EHG and some population of CHG which had been north of the Caucasus for thousands of years. This was mixture from the actual Near East.
 
R1b-M269 first pops up in Western Europe 4600 years ago. It was absent in EEF. No other Neolithic people came to Western Europe besides EEF, then in the Bronze age Steppe people with R1b came. This is all old news.

R1b pops up in 5000 BC EEF individual in Iberia. How was it absent in EEF?
 
I'm not clear about where you disagree with Lazaridis. He is saying CHG + EHG is rejected, while EHG + Iran Chalcolithic is not. He's also implying, I think, that they don't yet have the sample from the specific population which went north. If they did, the fits would obviously be better. During the Chalcolithic there were probably a number of populations in the northern Near East with slightly different mixes of ancestries. The one that did go north may have picked up more Levant or Anatolia EEF, but be relatively close to Iran Chalcolithic.

At any rate it's pretty clear, in my opinion, that Yamnaya is not a mix of EHG and some population of CHG which had been north of the Caucasus for thousands of years. This was mixture from the actual Near East.

I never said I disagree with Lazaridis. Did I give that impression? I said I agree with him that CHG can't be the "Teal source" of Yamna.
 
R1b pops up in 5000 BC EEF individual in Iberia.
Yes but V88 rather than M269.
 
In Bronze Age J2b and E1b also appear in Armenia. Also this site http://www.ancestraljourneys.org/copperbronzeagedna.shtml considers L1a samples as 'Copper Age/Chalcolithic'

The location of the L1a samples is this https://en.wikipedia.org/wiki/Areni-1_cave_complex

The location of the Kura-Araxes R1b sample is this https://en.wikipedia.org/wiki/Kalavan

In middle Bronze Age R1b is found here https://en.wikipedia.org/wiki/Nerkin_Getashen

In middle Bronze Age E1b appears in the same place

In late Bronze Age J2b appears near R1b and E1b https://en.wikipedia.org/wiki/Norabak

Thanks for the links.

L1a in a different location all together, but everything else pretty much around Lake Sevan.

All of those Y-HG's would be expected in in the Bronze age in that region.
 
R1b pops up in 5000 BC EEF individual in Iberia. How was it absent in EEF?

R1b-V88 is probably linked to WHG type of ancestry in EEF that found it's way into Africa and the Levant. You'll notice that Villabruna R1b (xV88, xM269) is WHG not EEF. These are old hunter-gatherer north Eurasian lineages who mostly died out.
 
This is what Llorente et al had to say about phenotype:

"The! phenotypic! attributes! of! GD13a are! similar! to! the! neighbouring! Anatolian! early! farmers! and!Caucasus!Hunter)Gatherers.!Based!on!diagnostic!SNPs,!she!had!dark,!black!hair!and!brown!eyes!(see!Supplementary).!She!lacked! the!derived!variant!(rs16891982)!of! the!SLC45A2!gene!associated!with!light! skin! pigmentation! but! had! at! least! one! copy! of the! derived! SLC24A5! allele! (rs1426654)!associated!with!the!same!trait.!The!derived!SLC24A5!variant!has!been!found!in!both!Neolithic!farmer!and! Caucasus! hunter)gatherer! groups! (5,! 21,! 26)suggesting! that! it! was! already! at! appreciable!frequency!before!these!populations!diverged.!Finally,!she!did!not!have!the!most!common!European!variant!of! the! LCT!gene!(rs4988235)!associated!with! the!ability! to!digest! raw!milk,!consistent!with!the!later!emergence!of!this!adaptation (5,!21,!23)."

http://biorxiv.org/content/biorxiv/early/2016/06/18/059568.full.pdf
 

R2 in Neolithic Iran is a big deal because R2 a mysterious mostly south Asian lineage today. Wait for geneticker to post reads for phenotype SNPs, most results are based on few reads. It does appear CHG/Iran were darker EHG because 4/4 EHG and Chalolithic Samara have 374F allele.
 
I did make my proposals in many posts. 1. PIE is from the Iranian Plateau, reached the Steppes via the Caucasus (influx from Iranian Plateau to Caucasus and Steppes supported by archeology) or via East of the Caspian. In this scenario Indo European might have evolved on the Iranian Plateau and the Steppes could be a secondary homeland to the major European branches of Indo European, while Hittite didn't even cross the Steppes but directly moved into Anatolia.
Or Indo European evolved after some Iran_Calcolthic dudes reached the Steppes and merged with the EHG of Samara.

2. Indo European could have a South_Central Asian origin in itself and reached the Steppes via East of the Caspian. If that is not the case at least the EHG individuals probably came from South_Central Asia and reached Samara via the East Caspian route.

Note South_Central Asia in this case for me is the region between Afghanistan, Uzbekistan, Turkmenistan, Kazakhstan and Tajikistan.

Yes, both first and second scenarios you give here have certain probability. People can be careful to avoid premature conclusions.

Two competing hypotheses Steppe (Kurgan) and Anatolian have their arguments. Grey and Atkinson (2003) using statistical methods developed by biologists found that Proto Indo European spoken 7,800 to almost 10,000 years ago. Their findings gave support to Anatolian hypothesis! Nine years later a larger team of scientists including the two mentioned using mathematical model for geographical spreading of viruses again gave support for Anatolian versus Kurgan hypothesis. In those days seems that Anatolian hypothesis triumphed.

After that two new scientific papers things changed (and someone can see it is not good make speedy conclusions).

Phylogenetic analysis by Chang et al (2015) using generally accepted language ancestries found that ancestor language originated about 6,500 years ago. Chang et al examined over 200 sets of words using present day and historical Indo-European languages, and through statistical modeling, they concluded that languages which first used these words began to diverge about 6,500 years ago. This backs Steppe hypothesis.

DNA study Haak et al (2015) confirmed migration from steppes, people who lived in Yamnaya 5,000 years ago are closely matched with Corded Ware people in (today’s) Germany 4,500 years ago. Massive migrations happened from steppe. According researchers eastern migrants could replace domicile population (on areas present days Germany). Yes, we knew this earlier, but always it is good when exact scientific results give confirmation.

After these papers someone can reckon triumph Steppe hypothesis? But mater is complex and knowledge lacks.

For example we don’t know about languages of Starcevo culture, Linear Pottery Culture etc. in Europe.

Wikipedia:
“There are different opinions about the ethno-linguistic origin of the people of Starčevo culture. According to one opinion, Neolithic cultures of the Balkans were of non-Indo-European origin and Indo-European peoples (originating from Eastern Europe) did not settle in this area before the Eneolithic period. According to other opinions, Neolithic cultures of the Balkans were also Indo-European and originated from Anatolia, which some researchers identified with a place of origin of Indo-European peoples.”

Renfrew, author of Anatolian hypothesis, in the light of new findings, considers steppes as secondary migration IE speakers to Europe and about 3,000 years later in regards first migration IE speakers.

There are more hypotheses, among them, Armenian, Paleolithic continuity, Vasconic etc.

Armeinan hypothesis also makes sense. For Armenian hypothesis Hak et al (2015) argue:

“The Armenian plauteu hypothesis gains in plausibility by the fact that we have discovered evidence of admixture in the ancestry of Yamnaya steppe pastoralists, including gene flow from a population of Near Eastern ancestry for which Armenians today appear to be a reasonable surrogate (SI4, SI7, SI9). However, the question of what languages were spoken by the "Eastern European hunter-gatherers" and the southern, Armenian-like, ancestral population remains open.”

And Paleolithic continuity by Alinei has its value. This hypothesis suggests that Indo-European speakers were native in Europe since Paleolithic. By the end of ice age IE language family differentiated in languages which many of them survived and developed till today. We can argue that archeological and genetic evidence missing but it is very good food for thoughts and contributes to our knowledge.

There are more different hypothesis. One of them is Vasconic hypothesis proposed by Vennemann. Vasonic people lived in Western Europe and gave names to rives and places. Basque is Vasconic language which survived.

According Klyosov and Tomezolli (2013) original language of R1b carriers wasn’t Indo-European. According authors R1b carriers arrived in Europe about 4,800 – 4,300 years ago and they didn’t speak IE languages, these languages spoke R1a carriers. Authors claim:

“During the period of 3000 - 2300 ybp many R1a tribes migrated with their IE languages from the Russian Plain to central, western and southern Europe bringing to Europe the peoples later called Germans, Italics, Greeks, Illyrians, Balto-Slavs, and Celts (the Hallstatt and La Tene cultures flourished between 2600 and 2400 ybp). We posit that some Arbin (R1b) peoples adopted the IE languages from the R1a bearers and, in exchange, introduced NIE loan words and grammatical structures.”

As authors claim Basque is language of R1b carries which survived and authors think Vasconic hypothesis has ground. Also they think R1a carriers migrated from Anatolia to Balkans between 9000-8000 years ago and they brought IE languages. In that way and Anatolian hypothesis according authors has ground. Authors disprove Steppe (Kurgan) and Paleolithic continuity hipotheses.

However till today nobody found ancient R1a in the Balkans and idea that R1a carriers brought IE language to the Balkans has not been proved. Vasconic hypothesis is not accepted in scientific community. Maybe author’s claim about original languages of R1b carriers as NIE (non Indo-European) is not priori mistaken but someone can claim same for R1a carriers. And they could spoke non IE once.

I will repeat languages don't go always with haplogroups, expansion of any language may not be caused by mass migration of newcomers, it can be only language expansion where local people of different origin adopt 'lingua franca' and their native languages disappear. Also, people (elite) who conquer any territory not always impose their language on local population. Massive migrations or conquering any territory are not necessary preconditions for language expansion, language can be spread in different ways.

At today’s level of knowledge (which can be changed with new discoveries and evidence) we can make link between Anatolian, Steppe and Armenian hypothesis, they does not have to be mutually exclusive. Better picture can be synthesis these three hypotheses.
 

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