Saturday, January 2, 2016

Deleted Transcript of "Eurogenes" Blog Session on Ancient DNA From the Neolithic

As some of you know, I have been banned from the "Eurogenes" blog for asking them too many questions about their devotion to the simplistic EEF-WHG-CHG evolutionary model for human prehistory in Europe.  Apparently, we are expected to believe, without corroborating data, whatever these guys tell us and manage to force into publication at Nature.  We are expected to believe that the Mesolithic of the Balkans and Southern Europe was totally replaced by EEF "farmers" from the "Levant."  Apparently, these academic researchers, "Chad::Spencer Wells", "Davidski::Wolfgang Haak", "Krefter::Jean-Jacques Hublin",  "Rob:Ron Pinhasi" and their partners in crime, can't handle some too hot to handle questions, so they just delete them.

For the record, here is the transcript from today's blog comment thread ( before Wolfgang deleted most of it):


Following up on Open Genomes' link

http://www.open-genomes.org/images/Omrak_et_al._(2016)/Omrak%20et%20al.%20(2016)%20Fig.%20S2%20K=12%20Worldwide%20PCA.png

According to this, none of the European countries have the non-steppe component in Yamna. Does that mean that Yamna didn't really have an input in Europeans, but it was rather Yamna-like people (West Yamna??)

January 1, 2016 at 11:01 PM

BloggerDavidski said...

Yamnaya is a mixture of EHG and CHG (maybe with a little WHG too). This is so obvious in formal tests that there's no point debating it.

ADMIXTURE shows all sorts of things depending on the data that it's fed, and most of it is irrelevant.

Central Asians have a lot of CHG and some EHG, and with strong local drift they create their own clusters, and then pull both ancient and modern Europeans into these clusters.

January 2, 2016 at 1:44 AM

BloggerAlberto said...

This does look like some amount of CHG admixture to me, though they lacked the CHG genomes to test directly. We'll see what it is exactly when the genomes are available, but these stats are pretty significant (NE1 is almost exactly an Anatolian Neolithic):

Denisovan Armenia_BA Kum6 ne1 -0.0574 -3.594
Denisovan Sintashta Kum6 ne1 -0.0353 -3.016

January 2, 2016 at 3:22 AM

BloggerDospaises said...

@Alberto

The files are already available at http://www.ebi.ac.uk/ena/data/view/PRJEB12155

January 2, 2016 at 4:20 AM

BloggerRoy King said...

@Chad and @Krefter,
I'm curious. If Kum6 lacks CHG, then how do you explain that (using the D statistics from the paper itself) Kum6 and many Bronze Age samples from Armenia and Russia share more than these same Bronze Age samples with the European Neolithic like NE1. My guess is that Kotias would likewise have increased sharing hence Kum6 would be associated with Kotias more than the European Neolithic samples with Kotias? This analysis is separate from the k12 admixture and the PC plots.

January 2, 2016 at 8:56 AM


@ Royking

Roy, I suspect that the stats that clear up the picture are these:
Denisovan Armenia_BA Kum6 Iceman -0.0162 -0.92
Denisovan Karasuk Kum6 Iceman 0.0047 0.419
Denisovan Sintashta Kum6 Iceman 0.027 2.097
Denisovan Mezhovskaya Kum6 Iceman 0.0269 2.122
Denisovan Yamnaya_RISE Kum6 Iceman 0.0299 2.353
Denisovan Andronovo Kum6 Iceman 0.0319 2.861

It is not the case that all LNBA genomes favour Kum6. In comparison to Iceman, which is a genome with no especial similarity to CHG, all the genomes favour Iceman, except for BA Armenia which continues to favour Kumtepe as a proximal source of its EEF ancestry which still makes sense based on geography and history.

Using figure 4A from the figure, we have the following list of the similarity of genomes to Kum6:

Gok2
Less similar than all other Neolithics to Kumtepe.

Iceman
More similar than all other Neolithics to Kumtepe.

Stuttgart
More than Gok2 and Ne1
Less than Iceman, CO1, ATP2

CO1
More similar than all but Iceman

NE1
Less than all but Gok2

ATP2
More than Gok2, Stuttgart, NE1
Less than Iceman and CO1

It is a striking testament to the sensitivity of D stats that we can rearrange these into an order, of decreasing similarity with Kum6, in which every single one of the previous stats can be made to cohere:

Iceman
CO1
ATP2
Stuttgart
NE1
Gok2

If it is indeed true that Iceman is the neolithic genome most similar to Kum6, (there is corroboration of that from Treemix in Fig 4b as well) and that LNBA genomes with neolithic ancestry share drift with Iceman to the exclusion of other neolithic genomes, then LNBA genomes will also share drift with Kumtepe to the exclusion of other neolithic genomes, even if Kumtepe carries no CHG.

I wouldn't say that this is proven, there is still some possibility for the Kum6 to have CHG, but the fact that Iceman is favoured over Kumtepe and Iceman has no CHG makes that somewhat unlikely, especially as CHG is split 24 kya from EEF, its not a recent ancestral population, and so even a little CHG shared between Kum6 and LNBA should be expected to bias the statistic very strongly against Iceman.

January 2, 2016 at 9:24 AM

BloggerMarnie said...

@ryukendo kendow

PCA is sufficient to suggest that more ancient DNA (Mesolithic and EN contexts) is needed from Sicily, Malta, Greece, Albania, Western Turkey, Bulgaria, Macedonia, Corsica, Sardinia, North Africa, Cyprus, Southern France and Iberia to continue on with any rational discussion about the emergence of the Neolithic in Europe.

Your sampling of the Mesolithic and Neolithic is too sparse to continue on without this.

January 2, 2016 at 9:56 AM

BloggerAlberto said...

@RK

If I understand you correctly, you mean that the increased shared drift between Kum6 and LNBA populations is not due to Kum6 sharing drift with CHG, but to it sharing drift with Iceman. This is certainly consistent with the stats, but it leaves 2 good questions:

- Why does Iceman share much more drift with LNBA (including Armenia BA, Yamnaya or Andronovo) than Early European/Anatolian farmers (or even MN ones like Gok2 with high WHG admixture)?

- And why does Kum6 share much more drift with Iceman than the early Anatolian farmers do?

An explanation could be that:

- Kum6 is clearly different from Early Anatolian farmers, but for an unknown reason (since it's not CHG/EHG admixture).
- Kum6 had direct input into Iceman's ancestors.
- Iceman-related populations had direct input into LNBA populations (including Yamnaya).

A bit convoluted, but possible both by time and geography. We'd still need to figure out what's the exact difference between Kum6 and early Anatolian farmers, though.

Alternatively:

- Kum6 has CHG/EHG admixture
- Iceman has increased affinity to CHG/EHG admixed populations compared to EEF, but not by admixture (reason unknown).

(When I refer to Iceman above, it also applies to CO1, but to a lesser extent).

I've seen Iceman behave strangely in some Dstats, like sharing a lot of drift with the Kalash, so I'm inclined to go for the second alternative. But who knows, maybe that increased affinity of Iceman/CO1/Kum6 to LNBA is real without any kind of (known) admixture in them.

January 2, 2016 at 10:19 AM

BloggerChad Rohlfsen said...

Balkan LN flow back into Anatolia?

January 2, 2016 at 10:25 AM

BloggerChad Rohlfsen said...

NE1 isn't the same as Anatolians either. NE1 is like Stuttgart.

January 2, 2016 at 10:30 AM

BloggerKristiina said...

I have also been wondering if in Europe, there was not only WHG but somewhere in the Mediterranean area (Italian Ice Age refuge ?), there was also another autochtonous component that started to spread northwards with the Neolithic expansion. However, this European component would also have spread to the Near East and North Africa while Anatolian and Near Eastern component travelled to Europe.

January 2, 2016 at 11:04 AM

BloggerMarnie said...

@ryukendo kendow
@Alberto

This kind of thinking, talking about the Neolithic in the context of samples from Kumtempe, Anatolia, and the Alps, with no data from important centers of the early Neolithic, such as Thessaly and Bulgaria, indicates that your research is heavily biased against examining the possibility that the Southern Balkans (as well as Anatolia) are important centers for the Early Neolithic.

It's very deliberate, sloppy and unethical.

January 2, 2016 at 11:08 AM

BloggerAlberto said...

@Chad

"Balkan LN flow back into Anatolia?"

Kum6 is from 4700 BC. Iceman from 3200 BC. In the absence of further evidence, I would suggest Anatolian LN flow into the Balkans.

"NE1 isn't the same as Anatolians either. NE1 is like Stuttgart."

I said almost, and that's quite precise. Don't nitpick when you were telling people to look at the stats but didn't take a look at them yourself. Kum6 is not a typical Anatolian Neolithic farmer, at least not stats-wise.

January 2, 2016 at 11:33 AM

BloggerKrefter said...

@Everyone,

There's no point for more discussion. We'll have to wait for genome-bloggers to analysis Kum6. In the ADMIXTURE he doesn't score in the CHG/ANI component, but it's much less popular than most CHG components, so he could have had CHG. The D-stats suggest he had a mysterious relationship with Otzei, Steppe, and Aremnia_BA, but that Steppe is closer to Otzei. PCA has him positioned significantly East of other EEFs, so once again he could have had CHG.

January 2, 2016 at 11:45 AM

BloggerKrefter said...

@Marnie,
"This kind of thinking, talking about the Neolithic in the context of samples from Kumtempe, Anatolia, and the Alps, with no data from important centers of the early Neolithic, such as Thessaly and Bulgaria, indicates that your research is heavily biased against examining the possibility that the Southern Balkans (as well as Anatolia) are important centers for the Early Neolithic.

It's very deliberate, sloppy and unethical."

From Turkey to Spain to Hungary to Germany to Sweden to Ireland, all early farmers descend from the same ancient Aegean stock. Neolithic Balkans won't be any differnt!! We lack aDNA from Italy and Balkans, everyone knows this. Once we do get it won't debunk the basics on Euro genetic history.

Everyone in Italy and Balkans from 5500 to 3000 or 2000 BC will be EEF. Then we'll see arrival of Steppe and unknown West Asian peoples(inclu. CHG) in 2000 BC or afterwards. By the Bronze or Iron ages we'll see people who are a mixture of all those elements and similar to modern Italians and Balkans(except Slavs, because they have lots of admixture that came in the Middle Ages from proto-Slavs).

Trust me that's what'll happen. When all we had were less than 8 ancient genomes, this is what I and most predicated. Nothing that has come out in ancient DNA has been a surprise.

January 2, 2016 at 11:50 AM

BloggerChad Rohlfsen said...

I am seeing a common pattern though. Affinity to those low quality genomes and those not fixed, when it comes to deamination. Those BA Armenians show SSA admixture in the 2-3% range, which isn't real. Iceman is the same story, and CO1, to a lesser extent. The Yamnaya Rise samples are the same story as well. I bet once this is run through, this genome will show ridiculous scores, not just because of low SNP count, but also damage/deamination giving high SSA scores. Wait until we have a decent quality genome from the area, at the same time. It will likely cluster with the Anatolians.

January 2, 2016 at 11:52 AM

BloggerMarnie said...

@Alberto

"Kum6 is from 4700 BC. Iceman from 3200 BC. In the absence of further evidence, I would suggest Anatolian LN flow into the Balkans."

Alberto, neither the archaeological record, nor the record within cultural anthropology, suggest unilateral interaction between Kumtepe and the Balkans.

January 2, 2016 at 11:53 AM

BloggerArch Hades said...

So does this mean CHG was making it's way into Anatolia? It's sounds from the Abstract that we have Standard EEFs/ENFs but with a sprinkling of CHG.

January 2, 2016 at 12:08 PM

BloggerMarnie said...

@Krefter

"From Turkey to Spain to Hungary to Germany to Sweden to Ireland, all early farmers descend from the same ancient Aegean stock."

Then prove it. Currently, you have no data from the Balkans, no data from the Mesolithic, except for a few sites in Northern and Western Europe.

"Neolithic Balkans won't be any differnt!! We lack aDNA from Italy and Balkans, everyone knows this. Once we do get it won't debunk the basics on Euro genetic history."

What history is that? The one in which you are saying that Irish ancestry is derived from the "Middle East" and "Bronze Age Southern Russia"?

"Everyone in Italy and Balkans from 5500 to 3000 or 2000 BC will be EEF."

Actually, to some degree, I don't disagree with you here. But you haven't demonstrated that, scientifically.

"Then we'll see arrival of Steppe and unknown West Asian peoples(inclu. CHG) in 2000 BC or afterwards."

The CHG people? You mean one sample from the Caucasus? This CHG sample doesn't change the results from the Omrak paper, which shows a gapping need for samples from the Mesolithic and Neolithic of the Balkans, Greece and Italy.

"By the Bronze or Iron ages we'll see people who are a mixture of all those elements and similar to modern Italians and Balkans(except Slavs, because they have lots of admixture that came in the Middle Ages from proto-Slavs). "

Yes, thank you, Krefter, I know this. But where not talking about the Bronze Age here. We're talking about the Mesolithic and Neolithic, and its time for you guys to get real about that.

"Trust me that's what'll happen."

I have no reason at all to trust you.


"When all we had were less than 8 ancient genomes, this is what I and most predicated. Nothing that has come out in ancient DNA has been a surprise."

Oh, like your predictions about racial purity?

Stop predicting.

Samples please.

January 2, 2016 at 12:11 PM

BloggerStrandloper said...

"And do not ever, under any circumstances...."

January 2, 2016 at 12:19 PM

BloggerMarnie said...

@Krefter

And no cooking the datasets either. I expect to see independent labs doing this work, and the papers not all reviewed by the same five people.

January 2, 2016 at 12:19 PM

BloggerMarnie said...

@Standloper

God forbid that anyone should question the Racial Puritans.

January 2, 2016 at 12:20 PM

BloggerChad Rohlfsen said...

Alberto. Copper working in the Northern Balkans pre-dates Western Anatolia.

January 2, 2016 at 12:22 PM

BloggerMarnie said...

@Standloper

Just in case you missed the irony in that last statement, I am in part descended from the Puritans.

January 2, 2016 at 12:22 PM

BloggerArch Hades said...

"Then prove it. Currently, you have no data from the Balkans, no data from the Mesolithic, except for a few sites in Northern and Western Europe."

It's already been proven for Greece which is part of the Balkans, we have several Neolithic genomes from Northern Greece ranging from 6,300 BC to 4,000 BC, they're essentially the same, early EEFs and Identical to the West Anatolian farmers.

http://eurogenes.blogspot.com/2015/11/first-neolithic-genomes-from-greece.html

January 2, 2016 at 12:23 PM

BloggerMarnie said...

@Chad

"Alberto. Copper working in the Northern Balkans pre-dates Western Anatolia."

Good point, Chad. But it's not just in the Northern Balkans that there was early copper working. There's also the Central and Southern Balkans to think about. Just poking around for an hour on Anademia.edu should help clarify this for you guys.

January 2, 2016 at 12:26 PM

BloggerRomulus said...

Wow it's nothing. I wish these people with access to labs capable of analyzing ancient DNA would quit goose stepping the stuff we actually care about and sequence some ancient Greeks or Romans.

January 2, 2016 at 12:29 PM

BloggerMarnie said...

@Arch Hades

"It's already been proven for Greece which is part of the Balkans, we have several Neolithic genomes from Northern Greece ranging from 6,300 BC to 4,000 BC, they're essentially the same, early EEFs and Identical to the West Anatolian farmers. "

Essentially the same. How much the same?

Where's the paper showing Dstats, PCS, Admixture, and fstats for these Northern Greek samples?

If you have samples from Northern Greece and Anatolia, why aren't you digging back into to the Mesolithic in these sites to see if the Neolithic emerged locally in these areas, or not?

That is the big question among Neolithic researchers, is it not?

January 2, 2016 at 12:30 PM

BloggerArch Hades said...

@Marnie

Almost exactly the same, The PCA is right here.

http://2.bp.blogspot.com/-7MtwyAGL9N4/Vlc7Axp7MxI/AAAAAAAAKNc/kmqUaEyPrR0/s1600/hofmanova.jpg

The Northern 'Greek' Neolithic are exactly like Anatolian Neolithics and also like EEFs from Central Europe and Oetzi only with slightly less [7-11%] WHG ancestry, and the only modern populations which show high affinity to them are Sardinians.

As for what the Paleo-Mesolithics Hunter Gatherers in Greece and the Balkans were like, I dunno. But my guess would be very different. They had very low population density and were essentially replaced.

January 2, 2016 at 12:37 PM

BloggerArch Hades said...

"Wow it's nothing. I wish these people with access to labs capable of analyzing ancient DNA would quit goose stepping the stuff we actually care about and sequence some ancient Greeks or Romans."

Eurogenes says we're getting Mycenaean Greek genomes this year. That'll be very interesting.

January 2, 2016 at 12:40 PM

BloggerMarnie said...

@Arch Hades

Mycenaean Greek genomes will be interesting, but if you are going to talk about the Neolithic, it should be obvious that you need genomes from sites that are local to the areas of the early Neolithic.

That would include Armenia, the Zagros, Thessaly, and other specific early Neolithic sites in Bulgaria, and Macedonia. More early sites in Anatolia and the Fertile Crescent would also be good. Genomes from early sites in North Africa, Sicily, Corsica and Sardinia would also be highly informative.

I realize that it is very difficult to recover DNA from these older sites. However, you can't keep making these emphatic statements about the dynamics of the Early Neolithic without genomes from the Early Neolithic.

January 2, 2016 at 12:51 PM

BloggerMarnie said...

@Arch Hades

"As for what the Paleo-Mesolithics Hunter Gatherers in Greece and the Balkans were like, I dunno. But my guess would be very different. They had very low population density and were essentially replaced."

On what basis do you make this statement?

January 2, 2016 at 12:53 PM

BloggerKrefter said...

@Marnie,

Last thing I'll say is: No one here is payed to say certain things, no one is raciest, and aDNA from SE Europe won't change anything.

You have reason to trust my predictions, because my predictions are almost always correct and most here agree What is posted here is valuable because many posters have a lot of knowledge on the genetics and pre-history. They aren't what you say they are. You should read this blog and once you mature start posting.

January 2, 2016 at 12:55 PM

BloggerGaspar said...

With Kum6 showing no CHG. Living on the Scamander river in NW Turkey ( Troad region )

With Hatti ( 2000BC )and Hittite ( 1700BC )texts showing zero semetic language in Anatolia.

One must revisit the old fables that the Hatti and Hitties came from coastal black sea Bulgaria.
KUM6 could also have come from there.

what relation does barcin and Kum6 have?

January 2, 2016 at 1:07 PM

BloggerArch Hades said...

"On what basis do you make this statement?"

Well the pre Neolithic genomes of Central, Western, and Northern Europe are nothing like the EEFs. They are a group who share's a common phylogenetic tie which we call WHG. So why would the pre Neolithic "indigenous" of Southerneastern Europe be so different?

The Neolithic package started in the Levant, made it's way into Anatolia and then into Greece and finally further into the interior of Europe. I don't think the indigenous people of Southeastern Europe say 10-15,000 BC will be like EEFs at all. I could be wrong, but that would mean Europe had two radically distinct forger populations who remained isolated from one another for 10's of thousands of years. I doubt it.

January 2, 2016 at 1:08 PM
 
BloggerMarnie said...

@Krefter

"No one here is payed to say certain things, no one is raciest, and aDNA from SE Europe won't change anything. "

You've already stated emphatically that you dislike Greeks. You've made statements that you think an admixture component actually represents a people: "the teal people". You've said that you think it is acceptable to make assumptions about the origins of the Neolithic without having any data on hand (with the exception of a few samples from Anatolia) from early Neolithic sites.

"You have reason to trust my predictions . . ."

I actually don't trust your predictions.

And I'm not that interested in reading this blog, except to understand the kinds of intellectual contortions you guys come up with to justify your "Just So Stories."

January 2, 2016 at 1:09 PM

BloggerDospaises said...

I'll repeat what Strandloper tried to remind everyone about. "And do not ever, under any circumstances...."

January 2, 2016 at 1:12 PM
Blogger
Marnie said...

@Arch Hades

"Well the pre Neolithic genomes of Central, Western, and Northern Europe are nothing like the EEFs. "

Yes, that is readily apparent from numerous publications.

"They are a group who share's a common phylogenetic tie which we call WHG."

Um. A group?

Mesolithic Northern European samples do not look exactly the same, from an autosomal perspective. "WHG" as you call it, I believe was ascertained against the Loschbour sample. But not every Mesolithic sample looks like Loschbour. For instance, Karelia does not.

"So why would the pre Neolithic "indigenous" of Southerneastern Europe be so different?"

They are not that different, on the grand scale of things. They are largely derived from the same Upper Paleolithic populations. Or were the authors of this paper:

Eppie R. Jones et al., Upper Palaeolithic genomes reveal deep roots of modern Eurasians. Nature Communications 2015

just smoking weed?

"The Neolithic package started in the Levant"

Not according to Reingruber. Also, Anatolia is not the Levant, so there are really not many archaeologists today who think that the Neolithic started in the Levant. The real question is: to what extent did the Zagros, Western Anatolia, Greece and the Southern Balkans contribute to the Neolithic?

The notion that the Neolithic *started* in the Levant is simplistic and outdated.

"I don't think the indigenous people of Southeastern Europe say 10-15,000 BC will be like EEFs at all. "

Then prove it. That's an emphatic statement. There is no reason to think the population of the Balkans was very low during the Mesolithic. (Just as there is no reason to think that the population of Italy, Sardinia, Southern France, North Africa, Iberia, Anatolia, the Zagros or the Levant was very low during the Mesolithic.)

"I could be wrong, but that would mean Europe had two radically distinct forger populations"

Why would there need to be two *radically* distanct forager populations. These populations could be differentiated simply on their ecozone specializations. Reindeer vs Red deer, vs caprines. That's simplistic, but more probable than trying to suggest that the population of Southern Europe was so low that it was almost completely replaced during the Neolithic.

January 2, 2016 at 1:30 PM
 
 Rob said...
     
            Chad
            I don't think copper working in SEE per se predates that in the near
            east, it's just that It became more advanced (independently) in the
            Balkans during the M5.

            January 2, 2016 at 2:26 PM
 

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