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Thursday, August 4, 2016

On the origins of the first farmers in Anatolia


Open access at Current Biology:

Summary: The archaeological documentation of the development of sedentary farming societies in Anatolia is not yet mirrored by a genetic understanding of the human populations involved, in contrast to the spread of farming in Europe [ 1–3 ]. Sedentary farming communities emerged in parts of the Fertile Crescent during the tenth millennium and early ninth millennium calibrated (cal) BC and had appeared in central Anatolia by 8300 cal BC [ 4 ]. Farming spread into west Anatolia by the early seventh millennium cal BC and quasi-synchronously into Europe, although the timing and process of this movement remain unclear. Using genome sequence data that we generated from nine central Anatolian Neolithic individuals, we studied the transition period from early Aceramic (Pre-Pottery) to the later Pottery Neolithic, when farming expanded west of the Fertile Crescent. We find that genetic diversity in the earliest farmers was conspicuously low, on a par with European foraging groups. With the advent of the Pottery Neolithic, genetic variation within societies reached levels later found in early European farmers. Our results confirm that the earliest Neolithic central Anatolians belonged to the same gene pool as the first Neolithic migrants spreading into Europe. Further, genetic affinities between later Anatolian farmers and fourth to third millennium BC Chalcolithic south Europeans suggest an additional wave of Anatolian migrants, after the initial Neolithic spread but before the Yamnaya-related migrations. We propose that the earliest farming societies demographically resembled foragers and that only after regional gene flow and rising heterogeneity did the farming population expansions into Europe occur.

Gülşah Merve Kılınç et al., The Demographic Development of the First Farmers in Anatolia, Current Biology, August 8, 2016, DOI: http://dx.doi.org/10.1016/j.cub.2016.07.057

See also...

PCA analysis: Neolithic Central Anatolians

The genetic structure of the world's first farmers (Lazaridis et al. preprint)

Early Neolithic genomes from the eastern Fertile Crescent (Broushaki et al. 2016)

85 comments:

Rob said...

Great study
They've got a pre-Ceramic site -Bonkoclu c. 8000 BC- hypothesised to derive from 'native' Anatolian foragers by archaeologists. It showed low diversity c.f. later Neolithic sites; suggestive of inflow from southeast (?Levant). MtDNA wise, it had 2 N1a, K1a and U3. It shows high ROH, on par with WHG (!) confirming the idea that it might have been an isolated south Anatolian forager community "going Neo". On PCA it plots closer to neolithic europeans than (later) Barcin, which is a much further west, again suggesting extraneous gene flow after 7600 BC into Anatolia
I haven't looked at formal stuff yet

Roy King said...

Very cool stuff! Boncuklu is the earliest hunter-forager to Neolithic site within walking distance from Catal Hoyuk. The authors make the case that Boncuklu which has N1a and K1a mtDNA and clusters with the European Neolithic samples is a palimpsest of the Neolithic migrants going to Europe. When the BAM files become available (if not already), it will be intersting to see if the Y chromosomes are G2a.

Davidski said...

Here's a PCA of Greece Late Neolithic Klei10 that Open Genomes uploaded (red dot).

https://drive.google.com/file/d/0B9o3EYTdM8lQX1ZCcXplN2pmMzg/view?usp=sharing

Looks like there were a number of genetic shifts in that region during the Neolithic and Copper Age; first to the south, then to the east.

Colin Welling said...

so it sounds like farming in anatolia grew out of the natives, who were naturally low in diversity. Since the only shift we here about is an increase in heterogeneity it sounds like when pottery came to anatolia, the native anatolians just started to cross mix with one another on a more frequent basis.

David, does this study confirm deep ancestral continuity for anatolian farmers?

Matt said...

@ Colin, yeah, interesting to see this implies early groups in Anatolia who were differentiated, lower in genetic diversity, but similar, seem to sort of fuse, enriching heterozygosity and decreasing ROH.

Also the earliest groups in Anatolia shift away from WHG and gain affinities to ME (though the evidence for this is a supervised ADMIXTURE based on moderns, and not, I think D / f).

That all seems more against the idea of early farming communities being hit by a very strong founder effect / bottleneck from a very few founders and more that absorption happened continuously, first of the EN farmers in Anatolia with each and possibly groups from the Levant, Caucasus, wider ME, and then perhaps 20-25% WHG they picked up as they moved through Europe leading up to the MN.

Olympus Mons said...

@Davidski.
And frustrating that there is no "Armenia neolithic" in the plots right? so much talk about ghost population that could be averted. ;)


Dave, do you know on average how many years it takes from the collecting of a DNA sample from a inhumation and its publication results? say, late 2013 sampling should be out by now, right? do you have any idea?

I mean, Goat/sheep dna collected at same time, was only published now... so, do you know if human ends up taking longer?

ryukendo kendow said...
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Karl_K said...

@Ryu

"Is that really the case? The increase in diversity and decline in ROH seem to take place with change in autosomal composition, so maybe this change can be mostly accounted for by admixture with a phylogenetically distinct group?"

Without 'diverse' examples from earlier, or many quite different genomes from a 'single group', then this is better called admixture.

ryukendo kendow said...
This comment has been removed by the author.
Karl_K said...

Exactly. Either large admixture with closely related groups, or less admixture with more distantly related groups.

The other option is that the first Anatolian farming groups quickly seperated into self contained groups for a long period of time before re-joining later. That seems a bit strange.

More data is necessary!

ryukendo kendow said...
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Kristiina said...

Kumtepe (Kum6) is H2a, and H2 has not been detected in the Neolithic Near East or Anatolia except for H2a1 Areni-1 (Bird's Eye Cave, yDNA L1a) 4330-3060 BCE in Armenia, and it is indeed Chalcolithic Armenian genomes that on PC map are closest to Early/Middle Bronze Age Seppe genomes compared to later Armenian genomes.

The earliest H2a that I have noted are from Khvalynsk II Samara Eneolithic 5200-4000 BCE H2a1, Late NE, 3400-3000, Calden Germany H2, Remedello 3483-3107 BC Italy H2a, Donez Catacomb Lisichansk Ukraine H2a1 and Donau Eneolithic Smyadovo Bulgaria H2a2, Dniepr Eneolithic Vinogradnoye Ukraine H2a2, Dnieper Yamnaya Kirovograd Sugokleya Ukraine H2a2 x2 and Manych Catacomb Temrta III Ukraine H2a2. Therefore, H2a seems to have originated somewhere in the area between Italy and Samara.

In this case the Caucasian wife theory seems not to work.

Matt said...

Ryu, well, my intuition is, if diversity is similar in an earliest Anatolian farming population to CHG and WHG, then it builds up, to me the simpler explanation is that there wasn't a reduction bottleneck / massive founder effect at a point before to the earliest farming population, and HG groups including the ones the Anatolian farmers came from just were generally small. You could I suppose have there being an earlier panmictic large Anatolian population, then some group within this population expands very quickly, then the founder effect is masked out by admixture, but it seems simpler to me at the moment that there just wasn't a founder effect in this manner. Or you could have them be replaced whole cloth by a autosomally similar population with a much larger population size, I guess.

I'm not sure what evidence there would be for a sudden population explosion anyway; my understanding is that early proto-farming groups like the Bonkolcu did not grow at very high rates.

Olympus Mons said...

@Kristiina,

" indeed Chalcolithic Armenian genomes that on PC map are closest to Early/Middle Bronze Age Seppe genomes compared to later Armenian genomes. " - you can repeat this as much as you want, nobody will listen.

And by the way. I am starting to think there was a population movement from the north Balkans to Anatolia and Caucasus by 8000/7000 BC and those were important to "my story"... Do you know anything about that region/period?

Simon_W said...

In the paper they claim that the Iceman/Remedello group was more similar to Kumtepe than to European Neolithic individuals. But is this possible at all with the PCAs we've seen? Both in David's and in the paper's PCA the Iceman/Remedello group is far away from Kumtepe. What we see in the PCAs is a small shift of the Iceman/Remedello/CO1 group away from Middle Neolithic and West Europan early Chalcolithic individuals towards Kumtepe, consistent with some admixture, though in David's PCA not even this direction is evident, it looks just as consistent with stronger Europe_EN affinity.

Simon_W said...

The PCA plot in the paper looks anyway rather different from David's plots, with early Neolithic Europeans like Starcevo and Stuttgart being closer to modern Maltese than to Sardinians. And EHG very close to modern Russians, but that's the usual projection bias I suppose.

Simon_W said...

I'm very ready to accept an additional Chalcolithic migration from Anatolia to Europe, since that's suggested by the D-stats. (And also by archaeology at that.) But on the whole these later migrants didn't differ a lot from the earliest ones, the difference seems to be quite subtle, but still strong enough to be detectable with formal stats. I think the Iceman when compared to modern populations is still closest to Sardinians, not to Sicilians or Cypriots.

Matt said...

A few odd statistics from D(Denisova,EHG,Neolithic,Iceman&Remedello):

D(Denisova, Karelia, Stuttgart, Iceman) = D: 0.0394, Z: 4.995
D(Denisova, Karelia, LBK_EN, Iceman) = D: 0.0429, Z: 4.898
D(Denisova, Karelia, Iceman, Bon001) D: -0.0773, Z: -4.758

Simon_W said...

So what I'm thinking is that this Chalcolithic migration isn't the end of the story of East Med/Anatolian migrations into southern/southeastern Europe. Sicilians, South Italians, Maltese, Cypriots and some Greeks must have received plenty of additional geneflow from West Asia at some time after the Chalcolithic, although this is also evident from the paper's PCA plot. And for example in the new PuntDNAL K12 calculator Sicilians and Calabrians have 13 - 14% of the Iran_N component, while CO1 had 0% of this component. In Hungary it starts to appear cautiously with late Bronze Age BR2 @ 1.23%, who as it happens had yDNA J2, hardly a coincidence.

Grey said...

Karl_K

"The other option is that the first Anatolian farming groups quickly separated into self contained groups for a long period of time before re-joining later. That seems a bit strange."

If you imagine the development of farming as a sequence of food-providing percentages i.e.
- stage 1: farming provides 10% of food
- stage 2: farming provides 20% of food
- stage 3: farming provides 30% of food
etc up to 100%

then a forager group turning farmer might become more static at the beginning of the process and maybe more endogamous as a result?

Maybe only when they got to c. 70-80%+ food provision from farming could they become mobile again?

(i.e. switched from 80% food from HG and 20% from farming to 80% from farming topped up by 20% from hunter-gathering)

#

Another aspect might be if pieces of the neolithic "package" developed in different places maybe only when all the pieces came together: wheat, peas, pottery, sheep, goats, cows etc was there enough pieces to get the food-provision percentage up to that c. 80% level that allowed for large-scale mobility?

#

so maybe

stage 1)

forager group A domesticate wheat - provides 20% of their food - makes them more sedentary and endogamous

forager group B domesticate peas- provides 20% of their food - makes them more sedentary and endogamous

forager group C domesticate cows - provides 20% of their food - makes them more sedentary and endogamous

stage 2)

small numbers of A, B, C traders bringing their piece of the package settle and mix with the other two

stage 3)

once all components are in place providing 80%+ food from farming then large scale farming expansions can occur

maybe


Simon_W said...

Judging from David's PCA, Kum6 really was very different from Anatolia_EN and Europe_EN, but it's influence in Europe presumably wasn't very strong. Though it's tempting to speculate that the relationship between the ancient Raetic language in the Alps and Lemnian goes back at that time. After all, Lemnos is close to Northwestern Anatolia and the Iceman lived where Raetic was spoken in antiquity.

Grey said...

Simon_W

"So what I'm thinking is that this Chalcolithic migration isn't the end of the story of East Med/Anatolian migrations into southern/southeastern Europe."

I think people may be too hung up on the

ME -> Europe

aspect of this and not enough on the possibility of

near-steppe -> both SE Europe & ME

e.g. Hyksos, Sea Peoples etc

#

Thing is if you made a graph of steppe military strength it would go from near zero when steppe foragers were pushed back by farmers from the viable farming land on the edge of the steppe to very high by the time they had cavalry armies and could directly conquer regions.

That means there will have been a point somewhere along that graph where they were a threat but not yet a conquest level threat (aka raiding) and we know from later periods what can happen when you get long periods of raiding e.g. Arab sea raids on coastal Europe - depopulation of regions that can't be defended and a move to the high ground.

So seems to me it is very likely that people around the near-steppe would have moved away from PIE/IE at some point.

#

Also C-T - did they disappear or did they move?

Grey said...

from previous thread h/t FrankN

"Actually, the interaction started earlier, as can be traced on the following Obsidian trade maps:"

http://www.archatlas.org/ObsidianRoutes/ObsidianRoutes.php

which is the sort of pre-existing trade routes that might have facilitated peas getting to the wheat farmers and wheat getting to the pea farmers.

Kurti said...

what I was proposing allot of times is that the region from Anatolia to the northern parts of the Iranian Plateau were populated by a WHG (Anatolia) and ANE (Iranian Plateau) like people. Until a third population (Basal Eurasian) moved up from the Iranian South coast or Arabia and merged with the other two creating the Anatolian farmers in the West and Iranian Farmers in the East.

The Anatolian "Forager" looks much more WHG like. Mark these words. Other are suggesting that Villabruna did come possibly from Anatolia or is at least of the same stock as this Bonuklu Forager.

Grey said...

FPT Open Genomes

"David, it's interesting that you're finding such a "ghost population" that connects all three groups, the Anatolian, Levantine, and Iranian Neolithic.

Would anyone like to speculate about how such a population relates to the radiocarbon dated sites and cultures found on these maps?"

just speculating based on the earlier post but could obsidian traders/artisans have formed a wide ranging trader caste that created such a link? i guess you'd need samples from the actual obsidian sites?


jparada said...

[i]The Anatolian "Forager" looks much more WHG like. Mark these words. Other are suggesting that Villabruna did come possibly from Anatolia or is at least of the same stock as this Bonuklu Forager.[/i]

Either Anatolia or the balkan i would guess.

capra internetensis said...

@grey

Tepecik-Çiftlik from this study *is* an obsidian trading site. But the remains are from the Pottery Neolithic era.

Grey said...

apols for spamming but one last thought on

"The other option is that the first Anatolian farming groups quickly separated into self contained groups for a long period of time before re-joining later. That seems a bit strange."

if for the sake of argument a pre-condition for developing farming was already being sedentary then large lakes might have that effect

if the lake HGs got much of their food from the lake they might already be largely endogamous among themselves because the surrounding non-lake HGs wouldn't know how to get food from the lake

if later the sedentary lake HGs developed one part of the neolithic package e.g. peas, that might make them more endogamous as now the non-lake HGs don't know how to get food from the lake or from farming either

eventually if the lake people develop farming to the extent where they can produce 80%+ of their food from it (possibly with extra crop types brought by traders) they can cut the umbilical cord with the lake and expand as farmers

Grey said...

capra

ty

Open Genomes said...

David and everyone, in preparation for the data from the ancient Central Anatolians Kilinc et al. (2016), I've done the analysis for Rev5, Early Central Greek Neolithic from Revenia 6438–6264 BCE (8448-8274 BP). Rev5 slightly predates the earliest samples from Barcin in Northwest Anatolia, so Rev5 is from the very earliest known European Farmer culture:

http://www.open-genomes.org/genomes/Hofmanova%20(2016)/Rev5/

The plink files for the Affy Human Origins Array and the Human Omni Express chip are here:
http://www.open-genomes.org/genomes/Hofmanova%20(2016)/Rev5/plink/Human_Origins_Array/
http://www.open-genomes.org/genomes/Hofmanova%20(2016)/Rev5/plink/OmniExpress-24/


Gedmatch IDs:
M380264 Rev5 Revenia, Central Greece 6438–6264 BCE (8448-8274 BP)
M072869 Bar31 Barcin, Northwest Anatolia 6419-6238 BCE (8429-8248 ybp)
M822045 Klei10 Kleitos, Central Greece 4230–3995 BCE (6240-6005 ybp)

M197341 WC1 Wezmeh Cave, Central Zagros Iran 7455-7082 BCE (9465-9092 ybp)

Karl_K said...

@Ryu

"So little admixture with more distantly related groups can cause heterozygosity to increase greatly?"

Absolutely. Without knowledge of the common alleles in an earlier or larger meta-population, you won't be able to say that the increase in heterozygosity came from within the group or from admixture with a different group. Unless you had an example of the admixing population as a reference.

Just imagine the whole process at a much smaller scale. Let's say you had 100 people from one interbreeding population, and then suddenly broke that population up into 10 populations of 10 people each, who were only able to mate within their own group for 10 generations, and there would only be 10 survivors at each generation.

Within each group you would have high numbers of runs of homozygosity due to inbreeding and drift. Each of the 10 groups would become fixed at different alleles, randomly. No amount of further breeding within a group of 10 could make them any more heterozygous at any position. The length of the runs of homozygosity can tell you a lot about the population history, but you need really high quality data, and multiple samples, to actually be sure of that history. (It could be that you are just looking at an unusual, particularly inbred family).

Later on, you check a genome from the same group and find it to be much less homozygous at all positions.

There are several ways to explain this.

Number 1. You just have much better data in the later samples, so that you can see more of the diploid genome. This would be an artifact.

Number 2. The sub-populations of 10 people joined together into a meta-population of 100, bringing most of the original allele diversity (and heterozygosity) back into one interbreeding population. This would be clear by comparison to the original population, before the fracture and drift.

Number 3. Admixture with an extremely divergent population introduced a lot of new alleles all across the genome that were never present before. Comparison to the original population (before drift), or a sample from the incoming admixing group, would show that the new alleles came from a seperate population.

Of course this analysis all depends on the quality of the data. Even with a pulse of admixture, if people were usually having only first cousin marriages, then they would still have large runs of homozygosity. But if you had 2 unrelated samples, they would be homozygous for different alleles, not the same ones.

Rob said...

@ Karl K
Which interpretation are you favouring (currently) for the PPN -> Neolithic shift for this specific sample set ?

Karl_K said...

@ Rob

I am favoring slow admixture from very distantly related populations.

The few genomes we have from very early Neolithic populations show them to be extremely diverse. Yet they clearly interacted with each other, as crops and animals spread between them.

Kristiina said...

Olympus, Balkans are very interesting from the metallurgy point of view and it will be very interesting if we get ancient yDNA from Vinča culture (5700–4500 BC) which provides the earliest known example of copper metallurgy. What archaeological culture do you have in mind when you point to a population movement from the north Balkans to Anatolia and Caucasus by 8000/7000 BC?

It is a pity that I cannot find information as to if Kumtepe (4700 BC) is H2a1 or H2a2, because as I said above, mtDNA H2a has been detected as follows: Early Eneolithic Smyadovo, Bulgaria (4500–3000 BC) H2a2, Early Eneolithic Vinogradnoe Moldova (4500–3000 BC) and Remedello Italy (3483-3107 BC) H2a (H2a2?). Instead, H2a from Khvalynsk II Samara Eneolithic (5200-4000 BC) is H2a1, and it is this Samara line which is detected in Areni-1 from Armenia (4330-3060 BC). From the point of view of the origin of H2a it is important that the oldest H2a2 is from Karelia as we have Yuzhnyy Oleni Ostrov, Karelia (5500 BC) H2a2b.

If Kumteke (4700 BC) is H2a2 it could have arrived to Anatolia from nearby Bulgaria and it could also explain why it is Sardinian and Oetzi like. However, I know that there are people who want everything to have originated in the Near East. In any case, Kumtepe site is said to be near Troy on the western coast of Turkey which means that it is very close to Bulgaria.

Alberto said...

@Matt

A few odd statistics from D(Denisova,EHG,Neolithic,Iceman&Remedello):

IIRC, Kurd did some double outgroup D-stats with Iceman and the chart was topped by Kalash and maybe even Yamnaya. So there's definitely something odd in the way Iceman behaves in D-stats.

But it's not the only case, apparently, since lately we've been seeing strange stats in several papers. Strange in the sense that they are different from the ones we've seen in other papers before, but then one starts to wonder which ones are the correct ones. Does Ötzi really have some strong EHG affinity? Because that shouldn't be impossible from its place and time, and it would be important to understand what was going on at the time.

But then in any PCA it seems to plot consistently with Sardinians, and IBS also shows the Sardinian affinity as highest, so I think these things are all strangeness of D-stats. But I wish someone from the teams running these stats would check what's going on there. Seeing such discrepancies in formal stats depending on who sequenced a genome or who/how runs that stats is not very reassuring.

Alberto said...

@Kurti

what I was proposing allot of times is that the region from Anatolia to the northern parts of the Iranian Plateau were populated by a WHG (Anatolia) and ANE (Iranian Plateau) like people. Until a third population (Basal Eurasian) moved up from the Iranian South coast or Arabia and merged with the other two creating the Anatolian farmers in the West and Iranian Farmers in the East.

Yes, I agree with you. The limited distribution of Basal Eurasian before the Neolithic and its possible lack of Neanderthal admixture (unlike all other Eurasians) does invite to think it's a late (LGM?) arrival to the main areas of Eurasia. Whether it came from deep down into Arabia (Yemen? Oman?) or somewhere in Africa itself is hard to know, but it's indeed unlikely to have been in the main areas of West Asia 30-40 KYA.

And then the genomes we have from Mesolithic and Early Neolithic West Asia already tell us with which kind of populations these Basal Eurasians admixed in each part. Plus this explains parsimoniously both ancient and modern distribution of those components.

Matt said...

OT: New bioRxiv stuff that may be of interest:

http://biorxiv.org/content/early/2016/08/04/067835 - "Signatures of human European Paleolithic expansion shown by resequencing of non-recombining X-chromosome segments" - identification of non-recombining portions of the X-chromosome that can be used to information population history like the Y-chromosome.

http://biorxiv.org/content/early/2016/08/05/067850 - "Overcoming the dichotomy: new insights into the genomic diversity of open and isolated European populations"

http://biorxiv.org/content/early/2016/08/02/043562 - "Complex ancient genetic structure and cultural transitions in southern African populations"

ryukendo kendow said...
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Olympus Mons said...

@grey,
Obsidian. - lets not forget that the "kings" of Obsidian assemblage were "my Shulaveri Shomu". The Ghost people (because nobody knows where they came from and why they were totally gone) known for Long Prismatic blade and Obsidian. Pretty much the wiki description of them.


Alberto said...

@RK

I found them, and they are double outgroup D-stats. But they were for Kalash, and Iceman was at the top:

http://www.anthrogenica.com/showthread.php?5387-Interesting-Ancient-Dstats&p=113026&viewfull=1#post113026

IBS of Iceman run by Davidski long ago appears normal, with Sardinian and Italian_Bergamo at the top.

I don't think it's specifically a concern about double outgroup, since the stats posted above by Matt show this strange high affinity to EHG in Iceman too. I don't know what causes some genomes to behave strangely, but that is a matter of concern for any paper using formal stats and should require some investigation.

Olympus Mons said...

@Kristiina,
I need to dig deeper in VInca (have bumped into them serveral times) but need to understand who were the one that predated Vinca and became Vinca. Because of Spelt.

I have dozens of these. Lets take Spelt (known as a trade mark of Bell beakers). Spelt being an Hybridization of emmer and bread wheat was a cereal that was part of the Neolithic but only with a select few. As far as I know earliest (5900 BC) confirmed Spelt was with Shulaveri-Shomu. Then later following the low lands near the caspien (Azerbaijan) it shows in north Iran. So pretty much same place. Then it shows at Merimda/El Omari in the Nile Delta (4500 bc). Then it shows at Iberia , at least, in copper age (2500 bc) and then with bell beakers.

Just learned yesterday that Spanish Spelt is actually Asia Spelt (So shulaveri Spelt)
-Analysis of Intraspecific Divergence of Hexaploid Wheat Triticum spelta L. by C-Banding of Chromosomes

However the Russian anthropology in the 60/70 always mentions an earlier Spelt in the Balkans. But since the grains can not be found anymore, there is a doubt. But they did mentined spelt in a Balkans culture (don’t remember which) that showed Spelt (so they said). Just something worth while checking.

Jaydeepsinh Rathod said...

Alberto,

Iceman/Remedello group seems to have some CHG related admixture as suggested from this latest paper.

"the Iceman/Remedello group was more similar to Kumtepe than to Boncuklu, Barcın, Tepecik-C¸ iftlik, or European Neolithic individuals. We further found that both Kumtepe and the Iceman/Remedello group carried more CHG alleles than other Neolithic populations (Figure 3C)."

CHG has some ANE affinity. Could this be a reason for Otzi to show preference for EHG ?

Matt said...

@ Jaydeep, the odd behaviour of those stats to me was is seems to show Iceman further from EHG than early Neolithic people in Europe are, though closer than Bon001 is.

Stats also go for:

D (Denisova, Satsurblia, Stuttgart, Iceman): D: 0.0318, Z: 4.046
D (Denisova, Satsurblia, LBK_EN, Iceman): D: 0.0265, Z: 2.984
D (Denisova, Kotias, Iceman, Bon001) D: -0.062, Z: -6.059

and:

D (Denisova, Bichon, LBK_EN, Iceman) D: 0.0524, Z: 6.449
D (Denisova, Bichon, Stuttgart, Iceman) D: 0.0378, Z: 4.904
D (Denisova, Bichon, Iceman, Bon001) D: -0.0734, Z: -6.464

Seem like indicate more sharing between CHG to Europe_EN and WHG to Europe_EN than Iceman, but also more sharing from CHG and WHG to Iceman than Boncuklu.

(Also:
D (Denisova, Satsurblia, Spain_MN, Iceman) D: 0.0548, Z: 6.486
D (Denisova, Loschbour , Spain_EN, Iceman) D: 0.0393, Z: 5.06)
D (Denisova, Loschbour , Spain_MN, Iceman), D: 0.0022, Z: 0.26) )

Kum6 gives... mixed signals to CHG compared to the above:
D(Denisova, Kotias, Kum6, LBK_EN) D: -0.041, Z: -2.471
D(Denisova, Satsurblia, Kum6, Bon001) D: -0.0167, Z: -0.621

These are from their http://www.cell.com/cms/attachment/2062474746/2064493943/mmc4.xlsx
Anyone else want to look at them and see if I'm reading them wrong, if you're interested.

Kristiina said...

My prediction is that we will find R1b-269(xL23) and a lot of mtDNA H in Vinča. Let's see how I will fare with my prediction.

Alberto said...

@Jaydeepsihn, Matt

Yes, the CHG in Iceman would explain the sign of the stat, but I was surprised by the magnitude of it. However, looking at the rest of the stats it seems that the increased affinity to Karelia is mediated by increased affinity to WHG and Iceman just behaves like Spain_MN:

Denisova Loschbour Spain_MN Iceman 0.0022 0.26
Denisova Karelia Spain_MN Iceman 0.0087 0.93

So that would be normal then. Though at the same time:

Denisova Kotias Spain_MN Iceman 0.0392 5.083
Denisova Tep002 Spain_MN Iceman 0.0432 4.243
Denisova Tep003 Spain_MN Iceman 0.0577 6.515

It seems a bit strange that Iceman manages to be equally related to WHG and EHG as Spain_MN is, but then being closer to CHG and Anatolia Neolithic than Spain_MN is.

Alberto said...

@Matt

the odd behaviour of those stats to me was is seems to show Iceman further from EHG than early Neolithic people in Europe are, though closer than Bon001 is

But those stats show Iceman being closer to Karelia than both EEFs and Bon001 are. Or am I not reading them correctly?

Matt said...

@ Alberto, IRC a *lower* stat on D(A, B, C, D) where A is the outgroup implies that population B-C more related than B-D. This is how past outgroup stats we've run have worked.

E.g. taking the most extreme negative Z score example from their D(Denisova, HG, HG, Anatolia):

D (Denisova, Bichon, Loschbour, Bon002) D: -0.2269, Z: -27.095
D (Denisova, Samara, Karelia, I1585_Barcin) D: -0.1289, Z: -10.626
D (Denisova, Satsurblia, Kotias, Bon002) D: -0.1144, Z:-14.797

or for comparisons with Bon001 as PopD

D (Denisova, LaBrana1, Loschbour, Bon001) D: -0.1609, Z: -14.972
D (Denisova, Kotias, Satsurblia,Bon001) D: -0.1058, Z: -9.375
D (Denisova, Karelia, Ajv58, Bon001) D: -0.0935, Z: -5.905

So those stats you gave with Spain_MN and Iceman would I think not imply that Iceman is closer to Kotias or Tep002/Tep003 than Spain_MN, but further away. Which seems to me not that consistent with the message of their paper?

Alberto said...

@Matt

But what do you mean by "a lower stat"? You mean lower than zero? That's how I understand it. But this one, for example:

Denisova Kotias Spain_MN Iceman 0.0392 5.083

Is not lower than zero, it's higher than zero. So shouldn't that mean that B-D share more alleles than B-C do?

Matt said...

Yeah, that's right actually. What was I thinking? ;(

batman said...

@ Kristiina:

"If Kumteke (4700 BC) is H2a2 it could have arrived to Anatolia from nearby Bulgaria and it could also explain why it is Sardinian and Oetzi like."

The H2 you mentioned in chronological order:

H2a2b:
Yuzhnyy Oleni Ostrov, Karelia (5500 BC)

H2a1:
Khvalynsk II, Samara Eneolithic (5200-4000 BC)
Areni-1, Armenia (4330-3060 BC)

H2a2:
Smyadovo, Bulgaria (4500–3000 BC)
Vinogradnoe Moldova (4500–3000 BC)

H2a:
Remedello Italy (3483-3107 BC)

---

Seems there's a bifurication of H2 appearing, branching into H2a1<->H2a2, in an area between Oleni Ostrov and Khavalynsk.

The branching of H2a seems to have happened before Oleni Ostrov (7.500 BP), Unless H2a1 (7.200 BP) is a derivate of H2a2...?

A simplistic interpretation from this groups alone are obviosuly pointing to Carelia as a basic sample to solve the question about the origin of mt-dna H2.

If the basis of interpretation is to be gentetic facts aand genetic facts alone.

---

@ Kristiina:

"However, I know that there are people who want everything to have originated in the Near East."

Darn sure.

"The Anatolian Neolithic Package" have been a straigth-jacket on the entire discussion about the origin of agriculture and - pr. consequence - "early civilization" since this model was i-n-v-e-n-t-e-d some 70 years ago.

To prove this hypothesis we've seen numberless throwels busy in and around "The Fertile Crescent", an area based on the Bay of Iskander, along the humid climate-zone following the southern heights of the Anatolian mountain-range from the NE Med into the arid deserts of Syria and Irak.

Picking this specific, but very limited brink-area of humidity and fertile soil - to be "the very origin of agriculture" - is obviously contradictory to 'common sense' as well as 'statistical probability'.

Though, it seems to fit well with a specific line of history-writing, known to grow out of the romantic views of the 19th century, known as "In Oriente Lux" and the consequent view shared by archeologists like Dr. Childe and Sir Wheeler.

Substantiating and comparing the discoveries of the (somewhat) contemporous 'high-cultures' in Egypt, Mesopotamia and the Indus Valley, Wheeler were the first to explain "The First Civilizations" - as the result of these 'high-cultures'.

Explaining the origin of the close parallels found between the rivere-deltas of the Nile, the Euffrat/Tigris and the Indus Sir Wheeler were unable to find a common source of proves of pre-agricultural contacts between the continents. In those days - between 1950 and 1970 - it was a videly held view that 'primitive man', before "the rise of civilization" where not able to travel and trade across such distances. Which made Wheeler poke a finger at his contemporaries in his book "The Indus Civilization":

"We do not know from where the first idea of civilization came. But ideas have wings, and the idea of civilization seem to have been in the air at the time of first Egyptians, Sumerians and Indians."

Later he added: "Archaeology is not a science, it's a vendetta."

Which still seem to have it's impact on the prestigous participants of the archaeological community, from where it keeps spilling into the field of human genetics, due to geneticians that forget to exercise proper source-criticism, but rather use the "general assumptions" and views based on "general consent" - within present archaeology - as factual premises of their own, genetical intrepretations.

Creating a bias that is nothing but confusing, counter-productive and dismal to the genetic profession. Which is why I keep insisting that the gentic results must - always - be interpretated (completly) independent from any 'opinion' and every 'common view' expressed by the present proselytes of the post-modern, post-processual and consentual archaology.

Alberto said...

Ah, ok, I got confused too wondering what was I missing in those stats.

In the end they look more or less normal, just that Iceman seems to be quite "central" and share drift with all the parts (or something in the way it's genotyped makes it seem like this, because those ones with the Kalash do look strange, but that's a different story...)

batman said...

"Dead archaology is the deadest dust that blows".

- Mortimer Wheeler

Today "The Idea of Cultivation" have been found, analyzed, documented and confirmed FAR and WIDE outside of "The Fertile Crescent" - such as South-America, China and Europe - during the veryu same time-frame as the first domesticates arrived the shores of the eastern Med and The Fertile Crescent - as a ready-made package...

Moreover, since Childe's and Wheelers's eminent works it's been discovered that the first samples of Cultivated Crops and Domesticated Animals - along with hand-mills, advanced pyrotech, baked ceramics and symbolic art - actually evolved within very stable and well-organised societies of paleolithoic Eurasia, not the least along the fertile soils of western and eastern Europe, from Solutrean to Kostenki and Sunghir.

Since the genomes of U-I, K17 and MA1 it's firmly established that paleolithic Eurasisa have been surprisingly homozygotic - from Spain to Siberia. Which explains that the experience and (consequent) knowledge of cultivating millet, barely and oat, as well as domesticating kids, cubs and calves - of goats and reindeers, horses and dogs - where practised across the arctic hemoisphere - where the harvest of the autum is defining who's to live and who's to die - as the sunshine darkens and the land gets covered in ice and snow...

Thus the evolution would turn the tropical gathering into arctical cultivation, as an intensification of food-production became nesseacary, where summers are short and winters long. Thus "cultivation and harvesting" - according to the yearly seasons - have always been a nessesity to survive in the arctic parts of the world.

As several signs of cultivation/doemstication are found in Eurasian settlements from the time of the Middle Paleolithic industry, in Europe known as the Micoquien.

https://en.wikipedia.org/wiki/List_of_domesticated_plants#/media/File:Feature2originmap600.png

60.000 yeasr old porridge, from neanders - or early caucasisans?
http://johnhawks.net/weblog/reviews/neandertals/diet/speth-slow-cooking-2013.html

60.000 years old flute from Balkan - courtesy of Neanders or Cro-magnons?
https://www.youtube.com/watch?v=sHy9FOblt7Y

Today we have to discuss the 'origin of agriculture' - as well as "stable and complex, art-producing cultures" and "The Origin of Civilization" - with an open mind.

That was exactly what the above mentioned pioneers did, to become celebrated professionals. Honoring their memory we better copy their professional ambitions and open-mindedness, rather than degrading their pioneering spirit by turning their results and text-books into canonical straigth-jackets.

Matt said...

@ Alberto: Only way I can (partially) defend my poor judgement is I was thrown by them switching the position of Iceman / Remedello from C to D in some of those stats :).

But yes, you're right. By these stats it does look like compared to many of the MN population the Chalcolithic Iceman and the Remedello are closer / same distance to WHG, and also closer to CHG. E.g. D (Denisova, KO1, Spain_MN, Iceman, D: 0.0254, Z: 2.833). So poss more admixture from all those sources, or their intermediaries, or at least same from WHG even though more from CHG like sources. The differences in closeness to Karelia compared to the MN actually look less significant.

Interesting in view of IRC a some methods to estimate WHG ancestry did not seem to place Iceman / Remedello / CO1 with as much WHG as Spain_MN / Ballynahatty / Gokhem (so I was wondering if the MN was a temporary "zenith" of WHG which receded by later Chalcolithic populations).

But if they'e getting stats showing they are as close, then perhaps that's because that additional CHG and thereby more recent Near East affinity is confusing the ability of ADMIXTURE or other methods to assign. (Also does make it slightly more complicated to estimate a Yamnaya fraction in populations using CHG affinity alone...).

Kum6 also gets some non-sig positive statistics WHG with some European_EN, like D (Denisovan, LaBrana1, LBK_EN, Kum6) D: 0.0339, Z: 2.116 and the Tepeiks like D(Denisova, LaBrana1, Tep002, Kum6) D: 0.0513, Z: 3.535 so there might be some two-way element there.

Also with Iceman closer to the Tepecik Anatolians, so presumably the Anatolian ancestry in earlier European farmers was slightly divergent from the Tepecik group? Maybe it was more like the Boncuklu group, though there are not the statistics to test that.

batman said...

From the paper:

"Our results confirm that the earliest Neolithic central Anatolians belonged to the same gene pool as the first Neolithic migrants spreading into Europe."

Just as expected. Now, from where did they come - and in which direction can be traced, via genetical results and genetical results ONLY?


"Further, genetic affinities between later Anatolian farmers and fourth to third millennium BC Chalcolithic south Europeans suggest an additional wave of Anatolian migrants, after the initial Neolithic spread but before the Yamnaya-related migrations."

What exactly suggest that the migration goes FROM Anatolia, rather than TO Anatolia?

Since the results of aDNA from the ME and Anatolia started to appear it seems obvious that the are have been a creole of both y-dna and mt-dna.

Just as it still is - to an even higher degree.

Compiling the aDNA from the region it seems obvious that the Fertile Crescent - between the arid areas of the Anatolian mountains and the Syrian/Levantine desert - have been a "sink" rather than a "source" of both male and female haplogroups. Since the days of the Natufians, already...

http://www.archatlas.org/OriginsFarming/Colledge/Slide04.jpg

Assesso1978 said...

Batman

So Agriculture was brought to the Near East, by European Neanderthals ?
You're series of barely comprehensible rantings are worrying . Have you been in touch with your case worker ?

Roy King said...

The BAM files are up at ENA and they do have Y data, so soon we'll be able to see if some or all are G2a.

Kurti said...

Batman said

"What exactly suggest that the migration goes FROM Anatolia, rather than TO Anatolia?"
I am not sure if you have much knowledge about archeology and have been following the recent genetic papers.

If you do there is no reason to explain why Anatolia is rather the source than a sinkhole of farmers.

Anatolian_Farmers are basically Levant_farmers(who themselves are descend of Natufians) with little more Anatolian_Forager admixture.

If you claim these people came TO Anatolia you are certanly claiming Natufians have their origin in Europe. Makes sense doesn't it since we all know Europe is known as a source and the Middle East as a sinkhole. (sarcasm off)

I can't believe that there are still people asking these kind of questions.

Kurti said...

"However, I know that there are people who want everything to have originated in the Near East."
Just like there are people, wo want everything to originate in Europe but which one makes more sense? the Middle East as a source or Europe.


Obviously the Middle East as the part of the world which is the crossroad into the rest of the world for almost all Eurasian.

Davidski said...

@Kurti

The Villabruna cluster is from the Balkans, not from Anatolia.

The Proto-Indo-Europeans came from the Eastern European steppes, not from the Zagros Mountains.

Samuel Andrews said...

Geneticker began posting Y DNA results for the new Neolithic Anatolian men. 1/1 G2a2.

https://genetiker.wordpress.com/2016/08/07/y-snp-calls-from-neolithic-central-asia-minor/

Matt said...

Kurti: Anatolian_Farmers are basically Levant_farmers(who themselves are descend of Natufians) with little more Anatolian_Forager admixture.

Levant farmers are modeled as with descent from Anatolian farmers and Natufians. It's likely there was a two way dynamic.

While batman is a bit mad, the bit you're talking about is also talking about why there is extra relatedness between later Copper Age European farmers and later Anatolians. Migration from Balkan farmers to Anatolia is not unlikely to be part of that.

The only time there is a strong reason to suspect Europe has been much a population sink, is when the LGM made that inevitable, and then later when farming first developed. Otherwise, that should not be the assumption.

batman said...

@ Kurti

Sarcasm is cheap. Try thinking, for a change.

The mariners that brought megaliths to Gobekli Tepe, ceramics to Catal Huyk and domesticates to Cyprus and Crete didn't originate between the northern tiers of the Sinai desert and the bare mountains of Anatolia. However much you like to believe so.

From the lack of objectivity in your comment it seems you have had problems in following the array of scientific publications that have shared rows of new facts and insights into these issues - over the last three decades. That's perfectly understandable, unless you have a professional relationship to contemporary anthropology and history.

Though, as you keep participating in this and other blog-discussions, one may presume that you're able to keep up with the RELEVANT surveys that make headlines in our common newspapers?

http://www.dailymail.co.uk/sciencetech/article-2325768/The-Minoans-Caucasian-DNA-debunks-longstanding-theory-Europes-advanced-culture-Africa.html

As the haplotypes from the old, initial cultures of the Mediterranean keeps comming forth it is becomming o-b-v-i-o-u-s that the genetic origin of their y-lines have a LCA within hg C/F, known to have originated among the arctic Caucasians of paleolithic Eurasia.

Seemingly, a large part of the ancient mt-dna from Mediterranean antiquity also seem to have an origin in the paleolithic Eurasia. Please note that the facts recently arrived from the archaeological and genetical professions have - once and for all - changed the premisses for the century-old discussion about the origin of "Cultivation and Domestication" - as well as the "Complex cultures and Civilisation".

However Kurti and the Pope may feel about it.

Rob said...
This comment has been removed by the author.
batman said...

@ Matt

Please understand that it's a distict difference between 'mad' and 'controversial'.

Just as there is a distinct difference between 'inprobable' and 'impossible', not to mention 'relation' and 'causation' or 'episte' and 'doxa'.

In the young branches of science - such as human genetics - a certain amount of epistomological hygiene is normally required.

https://www.academia.edu/2374876/Science_epistemology_ideology

batman said...
This comment has been removed by the author.
batman said...

@ Davidski

"The Proto-Indo-Europeans came from the Eastern European steppes, not from the Zagros Mountains."

The Minoan culture of Crete have long been considerd to be initial to the Greek/Roman cultures - and thus a hub for (the centum-part of) the "proto-IE". How does the steppe-motive correspond with the aDNA obtained from BA Crete?

http://www.nature.com/ncomms/journal/v4/n5/full/ncomms2871.html

As of lately, the highlands of Crete have been suggested as a 'genetic refugia'- where som older hgs could have survived the turmoils of BA and IA.

There's still some G2-lines existing on Crete. How do they match with the ancient G2-sequences that keep popping up from mesolithic/neolithoic sites around the Med?

Davidski said...

Minoans weren't Indo-Europeans.

batman said...

There is NO hard evidence allowing for such kind of conclusions. Which means there's no basis for blunt conclusions.

Thus I was referring to the c-o-n-s-i-d-e-r-a-t-i-o-n-s made by a number of professional linguists, who have analyzed the matter methodically for some decades already. Today the majority of them seem to be of the opinion that the Minoan was part of the "large I-E language-family. Whic btw fits very well with the archaeological records.

One of the authoritative scholars of Minoan today is the english scholar Gareth A. Owens. His conclusion is that the Minoan is a IE language of the Satem-branch. One may question that, but his overall classification is beyond doubt - as far as I have seen:

Quote:

"Beginning our research with inscriptions in Linear A carved on offering tables found in the many peak sanctuaries on the mountains of Crete, we recognise a clear relationship between Linear A and Sanskrit, the ancient language of India.

There is also a connection to Hittite and Armenian. This relationship allows us to place the Minoan language among the so-called Indo-European languages, a vast family that includes modern Greek and the Latin of Ancient Rome."

(enquote)


---

Whatever you may think of their language - my concern was NOT about the Minoan language, but about the Cretean samples of present and ancient (Minoan) haplogroups - and their possible relations to your defining Steppe-motive, from the LNE/BA of the Lower Volga and the Caspian steppes.

Isn't there any?

Open Genomes said...

David and all, here is the analysis for Bon002, Early Central Anatolian Neolithic from Boncuklu near Çatalhöyük 8279-7977 calBCE (10289-9987 BP). Bon004 is from right at the start of the Early Central Anatolian Neolithic, the very earliest known Anatolian Farmer culture:

http://www.open-genomes.org/genomes/Kilinc%20(2016)/Bon002/

The plink files for the Affy Human Origins Array and the Human OmniExpress chip are here:
http://www.open-genomes.org/genomes/Kilinc%20(2016)/Bon002/plink/Human_Origins_Array/
http://www.open-genomes.org/genomes/Kilinc%20(2016)/Bon002/plink/OmniExpress-24/

Gedmatch IDs:

M311970 Bon002 Boncuklu, Central Anatolia 8279-7977 calBCE (10289-9987 BP)

M380264 Rev5 Revenia, Central Greece 6438–6264 BCE (8448-8274 BP)
M072869 Bar31 Barcin, Northwest Anatolia 6419-6238 BCE (8429-8248 ybp)
M822045 Klei10 Kleitos, Central Greece 4230–3995 BCE (6240-6005 ybp)

M197341 WC1 Wezmeh Cave, Central Zagros Iran 7455-7082 BCE (9465-9092 ybp)

Bon002 had an unexpected eye color:
Bon002 M311970 eye color prediction

Try comparing the IBD of Bon004 at 100 SNPs and 1 cM with the others, and especially with:
M677694 Satsurblia
M603839 Kotias
M115616 I0867 Levantine PPNB
F999937 NE1 Starcevo
F999916 Stuttgart LBK

Is this what you expected from Anatolians at the cusp of the earliest Neolithic?

Davidski said...

Thanks, I'll check him out with my tools today.

When I test IBD I only use BEAGLE. That's about the best tool I've come across for the job. But it's a lot of effort.

Open Genomes said...

Y-DNA SNP calls for Boncuklu near Çatalhöyük and Tepecik-Çiftlik in Cappadocia:

Bon001 Y-DNA SNP calls Aceramic Neolithic Central Anatolia Boncuklu 8212-7952 calBCE (10222-9962 BP) G2a2b2b1a-PF3422

Bon004 Y-DNA SNP calls Aceramic Neolithic Central Anatolia Boncuklu earlier than 8300 BCE (> 10300 BP) G2a2b2b-PF3258

Tep003 Y-DNA SNP calls Epipaleolithic Central Anatolia Tepecik-Çiftlik (level 5) c. 6500 BCE (> 8500 BP) G2a2a-PF3159

(Tep001 has many negatives for all major haplogroups, and one reported positive, PF3174, is the last base in an isolated damaged read. It seems that hardly any authentic Y was extracted.)

batman said...

Seems the gentics confirms the archaeology:
http://www.thelivingmoon.com/43ancients/02files/Turkey_Gobekli_Tepe_003.html

Which may illustrate the dynastical nature of various y-dna-lines...
http://humansarefree.com/2014/04/the-origin-of-blue-eyes-ancient-gods.html

Davidski said...

Bon002 clusters with Early European farmers in the K7. But it's a noisy result, probably due to deamination.

K7 Bon002
AG3-MA1 0.76
Andamanese 0.24
Basal-rich 48.74
Oceanian 0.76
Southeast_Asian 1.14
Sub-Saharan 1.86
Villabruna 46.5

Grey said...

Kurti

"Just like there are people, wo want everything to originate in Europe but which one makes more sense? the Middle East as a source or Europe. Obviously the Middle East as the part of the world which is the crossroad into the rest of the world for almost all Eurasian."

I think the word "crossroad" may be the critical point.

option 1: everything starts in the middle east

option 2: individual pieces of the eventual neolithic package originate all over the place - Europe, Steppe, Himalayas, Middle East, India etc - but the middle east is the place (in West Eurasia at least) where they all came together *because* it is the crossroad.

So, personally I think after all the pieces came together in the middle east (because it's a crossroad) the region became the main source of further innovation from that base - and imo that is why people assume everything started there - but i think it's highly some of the individual pieces that made up the final package will have originated elsewhere.

Open Genomes said...

David, as you see, Bon002 is a very important result, because she lived at 8279-7977 calBCE looks just like a Starcevo or LBK farmer (what became of the Cardial people in Gedmatch?) but actually lived right near Çatalhöyük which existed from approximately 7500 BCE to 5700 BCE, and flourished around 7000 BCE. That's 500-700 years BEFORE Çatalhöyük.

Çatalhöyük - Wikipedia

Why would someone from South Central Anatolia from c. 8,100 BCE look almost the same as someone from Stuttgart Germany 5,100 BCE, 3,000 years later? And complete with a substantial portion of WHG admixture?

It's as if the "admixed" Early European Farmers were already admixed with "European" WHGs when they first started farming in Anatolia.

You could try to filter Bon002 for deamination, or rather, filter out alleles that are neither the known ancestral or derived states and also C>T and G>A. I can also generate a Human Origins Array file for bases with a read depth of >1, or any number you'd like. Of course there would be many fewer bases, but it may be "cleaner".

Any preferences for a read depth? (I have it set to "heterozygous" if >= 25% of the alleles are minor alleles.

Bon002 actually had a pretty high average read depth for an ancient genome (6.688) so restricting the read depth may actually work pretty well.

Any suggestions about filtering by read depth?

Open Genomes said...

David, here are the plink files for Tep002, Pottery Neolithic Central Anatolia Tepecik-Çiftlik (level 5) c. 6500 BCE (> 8500 BP):

http://www.open-genomes.org/genomes/Kilinc%20(2016)/Tep002/plink/

This is the best one of the lot for Tepecik-Çiftlik. The sequence is just 0.721x coverage, and there's not enough SNPs for Gedmatch, but it may be enough to plot it and run some calculators. I wouldn't necessarily trust some of the others from Tepecik-Çiftlik because they have extremely poor coverage.

This one should be a bit more CHG shifted than some of them from Boncuklu, but without much WHG. (Without WHG, even if Tep006 is a C-V20 like La Brana 1!) Maybe you can detect this and see what kind of "CHG" this really is ...

batman said...

@ Open Genomes

Congratulations. And thank you. You've been finding an important crux.

@ Grey

Obviously there's been a connection between various peoples to constitute the societies that are known to have been populating the ME during the first two millennia after Ice-Age, 10-12.000 years ago.

We do know - from hands-on, well dated archaeology - that a marine culture actually existed at this time. The people that populated the vast areas continent of Europe and N Eurasia had boats for rivers and boats for oceanic waters, as well as skis and dogsledges, fishing-lines and nets, lamps and lamp-oil, etc.

This flint- and foraging-culture were obviously a major cause to the re-population of Northern Europe, where their early descendant have been found and their latest descendants still roams.

Apparently the same mariners were part of the re-popualtion of SW and SE Europe, too - as well as NE Asia. Inlcuding the northern shores of the Mediterranean Ocean, down to the Levant and Egypt.

Thus we're back to the tradition from the epi-paleolithic boat-culture. To whom tool-making and masonry, as well as cultivation and domsestication was well known. Which is why we can find a "leap-frog-pattern" in the spread of agriculture across the northern side of the Med - from the Fertile Crescent to the humid valleys of Iberia and the Atlantic facade. As well as to larger island as Cyprus, Crete, Sicily, Sardinia and Corsica, Irland, England/Scotland and the Orkneys.

http://www.sciencemag.org/news/2014/06/first-farmers-were-also-sailors

From the agricultural evolution grows the early phase of the "hellenic cultures", resultinjg in the Roman, Greek and Egyptian dynasties. Pioneered by the Cretean boat-culture, that besides domesticated animals and plants could ship agricultural produce - before they invented the Minoan megaliths, masonry and architecture. As LNE turns BA the connection between the Mediterranean and the Baltic smiths and masons becomes obvious.

Since the discoveries of early art of amber in Mesopotamia and (some early, royal grave of) Egypt, followed by a contemporary developement of metalurgy, copper and bronze, it seems clear that the connections of travel and trade were well in place at the time the first Phoenicians came out of the Meds - to learn from the natives how to reach the tin-mines of Brittain.

As new discoveries keep occuring we get to know that the very pioneers of marine industry made their seaworthy ships from planks, already 8.000 yrs ago - IN Brittain:

http://digventures.com/2016/06/has-the-worlds-oldest-boat-building-site-been-discovered-near-the-isle-of-wight/

batman said...

(... cont.)

In his major work "Between The Oceans" Barry Cunliffe details the traderoutes of Mesolithic/Neolithic Europe - between the Atlantic facade, the Baltic, the Caspian, the Black Sea and the Med, through a 'evolution' of 7000 years. "Pretty undisturned, until Roman invasion."

According to Plato's records and Caesars annals the major expertise of ship-building, map-making and navigation were to be found at the Atlantic facade, between Bretagne and Brittan.

The eastern "Silk and Spice-routes" and the western "Amber and Oil-Routes" are still known, from a variety of sources - and as of lately also as object to public attention and modern travellers, known as 'tourists' and/or 'students'. Of similar interest - to tag the wherabouts of the pioneering populations of Post-Glacial Europe - is the first, known flint- and salt-mines, of which a number is known.

Thus there are a number of specific traits NEEDED to survive in the north, that must have existed during the entire period called "The Late Paleolithic", well before the establishment of Ust-Istim, Kostenki, Hohe Fells and Cro-Magnon. Otherwise non of them would have managed to populate the entire northern continent of Eurasia, from Iberia to Siberia.

A number of these traits are known to have spread south, as soon as the Ice-time were over - and the valleys and rivers between Northern and Southern Europe were possible to travel. Thus we see a very fast repopulation of all of northern Eurasia simultaniously, as soon as the Younger Dryas ends and the climate retrievs to "Alleroed-level".

The presence of "arctic traits" or "characteristics" in the Med have long been known, from a number of important sites. Göbekli Tepe not the least. Today this seems confirmed via the genetic results from ME/NE Anatolia.

Now the question is WHO ELSE were appearing in Anatolia and the northern Levant at the end of Ice-time - able to build, form and decorate megaliths.
As well as cultivating plants and domesticating animals_ to survive the harsh winters of the "Pre-boreal period" - at Göbekli Tepe and the coast of Iskander, as well as the islands outside of Norway - 11.600 years ago...

With todays genetics it should be possible to answer which tropical etnicity that ALSO occured at this "cross-road" at the start of Holocene, to produce the first generations of the "anatomically very modern" Natufians.

Kristiina said...

I managed to find out the mtDNA haplotype of Kumtepe. It is H2a3 which is found in particular in Dargins in Dagestan and in Armenians, as well as in Eastern/Northern Europe and also in Kenya (El Molo).
http://www.ianlogan.co.uk/sequences_by_group/h2a3-4_genbank_sequences.htm

Dargins speak a Northeast Caucasian language (http://titus.uni-frankfurt.de/didact/karten/kauk/kaukasm.htm), so we could tentatively think that also Kumtepe people spoke a Caucasian-type language.

Gioiello said...

@ Kristiina

From a phylogenetically point of view the mt H2a* of Remedello is the oldest,

@ batman

In your interesting hystorical excursus you lacked all the leftists from Cavalli Sforza and all the Stanfordists.
As many bloggers here use sarcasm, I think that anyone will be able to be harder than me, thus I give you a private letter of mine, where one of the person supposed is a notorious blogger and a creator of DNA.land. You said "In Oriente lux", but it is "Ex Oriente lux", i.e "From Middle east the light", that did mean firstly the light of their dark Gods.

Hi Tullio, you wrote on your Ysearch account:"J1a1a1(2014). J1b2b(2013). Formerly J1c3d. (L-147.1) I am of a Roman Jewish family. From at least the late 17th Century, my ancestors lived in what is now Frosinone Province, migrating from Veroli to Castro dei Volsci (1758) to Vallecorsa (ca. 1800) before immigrating to the United States in the early 20th Century. NOTE: I am a 6/6 match for the original Cohen Modal Haplotype(CMH) and a 17/22 match for the(2009)Hammer-Behar expanded haplotype", but there are no proofs of that, if not the desire to be a Jew and their obstinate proselithism, at least for making us believe that they contributed to the European gene pool. The same Biamonte, who seems the closest to you at the STRs level and says coming from a Jewish family converted even with that surname of German origin and he is not able to say more about his eventual previous Jewish surname. The same proofs you carry, the CMH and the extended one at 22 markers of Behar and Hammer are not worth a fig, because the STRs are deceitful, above all in hg. J.
But if we start from J-ZS3684 in the YFull tree (I don't speak here about the upstream subclades and about which I wrote a lot and we will see if J1 will be found in Palaeolitic Italy or not) we may see that:
1) J-ZS3684 formed 7000 years ago and has two samples (YF05329 NOR and YF04986 IND), thus we may think that they are due to the first expansion from Southern Caucasus with the first agriculturalists
2) We have 3 subclades formed 5800 years ago; a) J-Z18293, yours, which seems European and only J-Y23172, formed 4000 ya, has Middel Easterner descendants; b) J-ZS4312, which seems above all Italian and in a second expansion European; c) J-Z2314, above all Italian and Iberian and only from J-Y5399, formed 2600 ya, has a Jewish recent cluster; d) from J-Y12510, present in Iberia, we have the J-Y5148, formed 4700 ya and from which derived all the Arab J1.
Thus it is difficult to think that you are of Jewish origin and not the other way around and to continue to think that when we find an Iberian it is a Jew converted and not that Jews are introgressed in Europe also in those haplogroups that are thought Jewish par excellance.
Catullus wrote: "Miser Catulle, desinas ineptire, et quod vides perisse perditum ducas".
Fortunately that from Etruscans only the Liber Linteus survived and highly corrupted, otherwise perhaps someone would have thought making me speak Etruscan again.

Samuel Andrews said...

So modern Europeans are mostly a mixture of 3 drifted Late Paleo/Mesolithic populations. I say 3 because I haven't seen any data confirming EHG was drifted instead of a mixture of two drifted populations. Does anyone have anything to say about that?

Once we get more Bronze age European DNA, which will definitely tell us the origin of most modern geographic diversity, it'll be interesting if we could figure out how much genetic diversity within Europe is due to local drift vs differnt proportions of ancestry from the same drifted ancestors. Is Irish-specific drift the primary reason Irish are differnt from Spanish or is having differnt propositions of ancestry from the same Mesolithic ancestors?

Matt said...

@ Sam, that's a good question ("how much genetic diversity within Europe is due to local drift vs differnt proportions of ancestry from the same drifted ancestors").

When it comes to Irish vs Spanish, likely it's mostly from different ancient ancestors. I think the lion's share across Europe is realistically going to be from ancient differences.

But you can have populations who line up with similar relationships to ancient outgroups who are not closest to each other.

E.g. English tend to be similar to the ancient outgroups with Czechs, and to have different relationships to ancient outgroups than Irish and Scottish. However for fst (for what fst is worth as a measure), the fst from English-Czech and English-Irish is identical 0.001. So, net of the ancient outgroups differences, it would seem like English-Irish might be closer.

Another is that the South Slavic populations (Bulgarian, Romanian) look closer by fsts to Polish than they would be expected to be based on relatedness to the ancient groups. That seems likely to be due to drift.

E.g. take a model where a proto-Slavic population is mixed from these ancients, drifts a little acquiring some characteristic allele frequencies of its own, then mixes into other populations with varying levels of ancient ancestry. They will then have more similarities in the allele frequencies than would be expected from their ancient ancestry alone.

There is probably some degree to which there is allele divergences are due to having similar ancient ancestry and recent ancestry.

Although people can always raise the objection that there could be some subtle substructure among the ancient groups which we don't currently have a definition for.

Gioiello said...

@ Kristiina
"I managed to find out the mtDNA haplotype of Kumtepe. It is H2a3 which is found in particular in Dargins in Dagestan and in Armenians, as well as in Eastern/Northern Europe and also in Kenya (El Molo).
http://www.ianlogan.co.uk/sequences_by_group/h2a3-4_genbank_sequences.htm"

It is possible that the true mutations of Kum6 (6700 YBP) are

T152C A263G 315.1C A750G A8860G T10810C A15326G G16274A T16519C

i.e. those found so far in

1. AM263180(Dargin) Roostalu H2a3 14-JUL-2008
T152C A263G 315.1C A750G A8860G T10810C A15326G G16274A T16519C

but also in Italy

2. AY738962(Italy) Achilli H2a3 13-APR-2007
T152C A263G 315.1C A750G A8860G T10810C A15326G G16274A T16519C

It seems unchanged after 6700 years. As mt hg. H2* seems older in Italy and Europe, I wouldn't been sure that the origin is in Anatolia rather than in Europe. Of course Anatolia has so far the advantage of the aDNA sample, but let's wait...

Gioiello said...

Of course it is also possible that Kum6 hasn't the mutations in 152C 10810C and 16274A and is a true H2a*.

Gioiello said...

From the paper: "The Kum6 mitochondrial genome has 39 mutations classifying it as haplogroup H2a (Table S3b). Twelve additional mutations were found in the consensus sequence. One of these is G16274A, which together with T10810C, defines subhaplogroup H2a3. Therefore, Kum6 seems to be an ancestral lineage to H2a3 as it has acquired the defining transition at nucleotide position 16274 but lacks the back mutation at nucleotide position 10810. Nine of the remaining additional mutations are supported by only one or two reads and the majorities of them are unique and not present in PhyloTree. Further, eight of these mutations are C to T or G to A transitions that can likely be attributed to post-mortem damage alterations [S69]. The last additional polymorphism, A6527G, may be a true mutation in Kum6 as it, like most of the 39 haplogroup defining mutations as well as the transitions at nucleotide position 10810 and nucleotide position 16274, is covered by >10 sequence reads".
Thus we should think to these mutations:

T152C A263G 315.1C A750G A6527G A8860G A15326G G16274A T16519C

i.e. a line pre-H2a3 very likely extinct.