Early Neolithic Pastoralist from the Zagros, Iran

A little late and definitely overshadowed, this is the paper that the leak was about, and that was discussed here:

http://www.eupedia.com/forum/thread...and-Turksih-Farmers-were-Genetically-Distinct


The genetics of an early Neolithic pastoralist from the Zagros, Iran
Llorente et al

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

"The agricultural transition profoundly changed human societies. We sequenced and analysed the first genome (1.39x) of an early Neolithic woman from Ganj Dareh, in the Zagros Mountains of Iran, a site with early evidence for an economy based on goat herding,ca. 10,000 BP. We show that Western Iran was inhabited by a population genetically most similar to hunter-gatherers from the Caucasus, but distinct from the Neolithic Anatolian people who later brought food production into Europe. The inhabitants of Ganj Dareh made little direct genetic contribution to modern European populations, suggesting they were somewhat isolated from other populations in the region. Runs of homozygosity are of a similar length to those from Neolithic Anatolians, and shorter than those of Caucasus and Western Hunter-Gatherers, suggesting that the inhabitants of Ganj Dareh did not undergo the large population bottleneck suffered by their northern neighbours. While some degree of cultural diffusion between Anatolia, Western Iran and other neighbouring regions is possible, the genetic dissimilarity of early Anatolian farmers and the inhabitants of Ganj Dareh supports a model in which Neolithic societies in these areas were distinct."

I'm still re-reading part of the Lazaridis Supplement, so I don't know when I'll get to this, but if some of you haven't seen it, I thought I'd provide the links.

Hmmm, so do they claim that there was no genetic connection between Iranian Neolithic Farmer with Anatolian Farmer? Check Figure C at the end of the paper:
http://biorxiv.org/content/early/2016/06/18/059568.full.pdf+html


If so it stands in contrast with recent Lazaridis paper claiming 40% autosomal input of Iranian N in Anatolian Neolithic farmer.
However, I would guess from Lazaridis PCA chart Figure 1b and 1c, no connection, but their predictor shows almost 40% connection to Iranian N, Figure 4b.
http://biorxiv.org/content/early/2016/06/16/059311

LeBrok said:

Hmmm, so do they claim that there was no genetic connection between Iranian Neolithic Farmer with Anatolian Farmer? If so it stands in contrast with recent Lazaridis paper claiming 40% autosomal input of Iranian N in Anatolian Neolithic farmer. I would guess from Lazaridis PCA chart Figure 1b and 1c, no connection, however their predictor shows almost 40% connection to Iranian N, Figure 4b.

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Maciamo's mtDNA analizes supports gene flow from Iran_N to Anatolian_N, but not from Levant_N/Natufian to Anatolia_N.

From Lazaridis Supplement Info page 110:

Table S7.25: Mixture models for Ancient West Eurasian populations. This is a compilation of thebest identified mixture models in this section (supported at the P>0.05 level). Mixture modelssupported at only a 0.05>P>0.01 level are listed in italics.

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Below this statement on page 110 is a table (can't post it), and the only entry in Italics is about Anatolian N, being half Iran N and half Levant N. It means the certainty of their modeling of ancestral population of Anatolian N, is of a very low reliability.

All other signs like PCA distances, or allele distances, and few other distances (pages 66,70,76,79,93,104 among others) always show Levant Neolithic and Anatolian N (also Natufians and European N) very close to each other. Unlike Iranian Neolithic which is usualy the farthest thing away.

I'm having serious doubts that Anatolian Neolithic contains any substantial (over 5-10%) of Iranian Neolithic gene pool. Actually this paper Llorente et al might be closer to the truth about Anatolian farmers being unrelated to Iranian one. Either Anatolian farmer is from Levant, or is a very close cousin of Levant farmer, who developed farming on their own. Most likely it is an "immigrant" farmer from Levant who mixed with 10% of WHG in Anatolia, and perhaps 5-10% with Iranian Neolithic farmer.

LeBrok said:

Either Anatolian farmer if from Levant, or is a very close cousin of Levant farmer, who developed farming on their own. Most likely it is an "immigrant" farmer from Levant who mixed with 10% of WHG in Anatolia

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It'll be interesting to see genomes from Mesolithic Anatolia and Greece and near by parts of West Asia. I agree Anatolia_N is probably cousin of Ancient Levant+WHG. That's what PCA suggests. Natufians and Levant_N are the mysterious pure ancient Near Eastern "EEF" people we've been waiting to get DNA ever since 2013(when Loschbour, Stuttgart, Motala DNA was sampled). They lack African and ANE and excess WHG ancestry.

LeBrok said:

Maciamo's mtDNA analizes supports gene flow from Iran_N to Anatolian_N, but not from Levant_N/Natufian to Anatolia_N.

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Not exactly. What I said was that the mtDNA supports gene flow from Anatolia_N and/or Iran_N to Europe. It could have been different migrations or the two groups could have merged in Anatolia before migrating west to Europe. We don't have enough mtDNA samples at present to determine if Neolithic East Anatolians and Iranians were similar or very different. What is certain is that all their mtDNA ended up in Neolithic and modern Europe, one way or another.

Maciamo said:

Not exactly. What I said was that the mtDNA supports gene flow from Anatolia_N and/or Iran_N to Europe. It could have been different migrations or the two groups could have merged in Anatolia before migrating west to Europe. We don't have enough mtDNA samples at present to determine if Neolithic East Anatolians and Iranians were similar or very different. What is certain is that all their mtDNA ended up in Neolithic and modern Europe, one way or another.

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We have an answer for this in ancient mtDNA. It came in two differnt waves. Iran/Caucasus one went to Russia and the Anatolia one went to the rest of Europe then they merged in 3rd millenium BC.

EDIT: How do you know so much about mtDNA? I saw your post about the new ancient Middle Eastern results and I'm surprised how you knew where those deep subclades are found. It took me a year really to gather the data needed to know that and if it weren't for haplogrep I wouldn't have been able to.

Fire Haired14 said:

We have an answer for this in ancient mtDNA. It came in two differnt waves. Iran/Caucasus one went to Russia and the Anatolia one went to the rest of Europe then they merged in 3rd millenium BC.

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That's not at all what the data says. The link between Iran and the Steppe is only evident for the Chalcolithic Iranian samples (H2a1, I1c and U4a), not for the Neolithic Iranian samples (J1c10 and X2), which are found among Neolithic Europeans but not in Bronze Age Steppe cultures (except for a single X2 in Yamna,).

EDIT: How do you know so much about mtDNA? I saw your post about the new ancient Middle Eastern results and I'm surprised how you knew where those deep subclades are found. It took me a year really to gather the data needed to know that and if it weren't for haplogrep I wouldn't have been able to.

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I have spent many years studying mtDNA haplogroups, in as much depth as Y-DNA haplogroups. I have written pages for each haplogroup, analysed the whole phylogenetic tree for each haplogroup, checked the regional data for each subclade, made maps... Then I tend not to forget things once they are inscribed in my mind.

Maciamo said:

Chalcolithic Iranian samples (H2a1, I1c and U4a)

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So, those H2a1, I1c and U4a, where do they originate? Steppe? North of Steppe? Central Asia? Syberia?

arvistro said:

So, those H2a1, I1c and U4a, where do they originate? Steppe? North of Steppe? Central Asia? Syberia?

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We cannot know at present. But all of them seem to be well represented around the Caucasus, and especially the North Caucasus.

Maciamo said:

We cannot know at present. But all of them seem to be well represented around the Caucasus, and especially the North Caucasus.

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Yeah, checked eupedia's mtdna. Caucasus and some Volga people groups have hotspots of those. Some Caucaso-Uralic link
Funny enough they (I and U4, not sure about H2, since dont know how our H is divided) are also (relatively) hotspoted in Latvia, but not really in other Baltic states.

Maciamo said:

That's not at all what the data says. The link between Iran and the Steppe is only evident for the Chalcolithic Iranian samples (H2a1, I1c and U4a), not for the Neolithic Iranian samples (J1c10 and X2), which are found among Neolithic Europeans but not in Bronze Age Steppe cultures (except for a single X2 in Yamna,).

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The data I'm referring to is ancient European mtDNA. Neolithic "EEF" people and Bronze age "Steppe" people had distinct mtDNA gene pools and several specific haplogroups don't appear outside of the Steppe till Steppe migration. These haplogroups today are European-specific and we can see looking at ancient mtDNA they arrived in a differnt wave than the European-specific mtDNA found in Neolithic "EEF" people.

Neolithic Iran/Mesolithic Caucasus-like people contributed a lot of ancestry to "Steppe" people but didn't contribute ancestry to Neolithic Europe. J1c in Neolithic Iran is a happy coincidence and is reflective of pan-Middle Eastern shared ancestry. Iran/Caucasus contributed mtDNA to Steppe, then from the Steppe to Europe.

The dubious claim that exo-migrating Iranians confined their movement NW through the Caucauses and into India, but strangely decided against moving Westward into Anatolia, is unfounded. One needs very little peripheral evidence, to reject such a notion. In fact, the IE influence from NW Iran, into Turkey, the Caucauses, the Steepe, and ultimately into western/central/southern Europe, is glaring. PC Plots from large scale studies, always reveal Turks and Iranian populations to be adjacent. The latter also being an extension of the populations of the lower Caucases. Only studies that lack genetic sampling, usually with only a few Y or mtDNA markers, is it possible to draw the erroneous conclusion that Iranians and Turks are significantly distinct. Unfortunately, similarly deficient notions have become more of a convenience towards defending the archaic steppe theory, among increasingly butt-hurt Steppe theorists.

A proper interpretation of the data presented in the study, is that Neolithic Iranians (or possibly only those restricted to Ganj Derah), only AS EARLY AS 10kybp, did not contribute European gene pool. This does not rule out the likely possibility that later Iranian Neolithic peoples, and Iranian populations onward, did not. Just based on the significantly more eastern position of Modern European samples (relative to older population samples), in the figure, it's pretty clear, in fact, that the total Iranian contribution to the European gene pool is greater than the authors conclude. The study is among other vile attempts to "Westernize" the origin of the modern European gene pool.