Broushaki et al, Early Neolithic Genomes from the Eastern Fertile Crescent

[Angela]

I know we have a thread on the yDna, but I can't find a thread on the paper as a whole. If someone can find one or knows of one we opened on the paper as a whole, could you let me know so I can combine the threads? I could swear I posted on it myself, but I spent a half hour searching and couldn't find it.

This is the thread predominantly on the yDna:
http://www.eupedia.com/forum/threads...593#post484593

This is the paper as a whole:
Broushaki et al, "Early Neolithic Genomes from the Eastern Fertile Crescent":
http://science.sciencemag.org/conten...cience.aaf7943

"We sequenced Early Neolithic genomes from the Zagros region of Iran (eastern Fertile Crescent), where some of the earliest evidence for farming is found, and identify a previously uncharacterized population that is neither ancestral to the first European farmers nor has contributed significantly to the ancestry of modern Europeans. These people are estimated to have separated from Early Neolithic farmers in Anatolia some 46-77,000 years ago and show affinities to modern day Pakistani and Afghan populations, but particularly to Iranian Zoroastrians. We conclude that multiple, genetically differentiated hunter-gatherer populations adopted farming in SW-Asia, that components of pre-Neolithic population structure were preserved as farming spread into neighboring regions, and that the Zagros region was the cradle of eastward expansion."

Razib Khan has opined on it here:
"The World After The Great Mixing":Sargon’s world is one whose outlines we are only vaguely aware of. There are many lacunae, not least of which the origins of the Sumerian people, who served to Sargon’s Akkadians the role of cultural progenitors. A linguistic isolate, the origin of the Sumerians is an unresolved mystery to this day. The end of the Sumerian cultural hegemony occurred in part due to the depredations of the Gutians, people from the hills of what is today Kurdistan, and rivalry with the people of Elam, from modern day Khuzistan.The linguistic affinities of the Gutians are unknown, while the Elamites, like the Sumerians, seem to be part of a linguistic isolate.
Much of this ignorance has to do with the importance of literacy in history. What we know about Elam is often through a Mesopotamian lens. The people of Sumer and Akkad, and later Babylonia and Assyria, saw Elam as the great enemy, the Persia to their Rome. The Gutians were a coalition of tribes from the mountainous areas to the east of Mesopotamia, and so had no real indigenous literate tradition. They do not even seem to have a distinctive enough archaeological tradition to trace their migrations. Without texts and material, where does that leave us."

A few more pertinent bits:

" I predict that when the first results come back from Elamite Iran there will be a strong affinity to peoples in southern Pakistan, especially the Baloch and Brahui, as well as connections to India more broadly, above and beyond the expected local continuity."

What do some of you think of that?Also...
"There were, it seems, two major phases. The first phase was expansionary. The western farmers pushed outward to Europe and North Africa. The eastern farmers pushed toward South Asia and Central Asia. But look at the position of Iranians in the PCA, and the affinities within Iran. Modern Iranians are much more west shifted than you might expect from perfect continuity. Additionally, the haplotype affinities of populations to western vs. eastern farmers shows that Iranians today have much more affinity to western farmers than Iranian speaking people from Pakistan, especially the Baloch and Makrani in the southwest of the country. This is because there was a second phase: the great scrambling, when reflux from the west into Iran, and vice versa, erased the great division.In the initial expansionary phased a stylized model was probably as good as any model. The world was dominated by hunter-gatherers, whose social-political ability to scale and organize was minimal. The farming populations probably began to organize chiefdoms rather early, and the spread of their lifestyle was to some extent at the tip of the spear. The hunter-gatherers fled, or were rapidly assimilated as subordinates, losing their cultural distinctiveness. But the next stage after the chiefdoms were more complex arrangements, which might transcend tribal loyalties, especially when one’s tribe spanned a continent."

"A close look at the map shows that the Baloch and Sardinians have more affinity with these two ancient peoples than many of the groups which today occupy the Middle East. Why? Mostly because they are distinctive in being less subject to the reflux migrations in the wake of the Neolithic. And, if you look at Europe and South Asia, you can see that Indo-Europeans also left a stamp on these areas, by mediating gene flow from these tribes into areas where the other tradition had been dominant. Northern Europe is less biased toward western farmers than Southern Europe. Within South Asia, the most skewed bias toward eastern farmers are the Baloch, who happen to co-inhabit territory with a non-Indo-European speaking population, the Brahui. These Dravidian speakers are basically indistinguishable from the Baloch."

We've said much of the above here on this Board, I think, although I personally had not thought of it as the Indo-Europeans bringing different farmer ancestry to Europe and Central Asia/South Asia.

[Angela]

This is what Khan has to say about the phenotype data in the paper.:

"But there are some intriguing elements of the pigmentation genetics, a topic I know a fair amount about. The results from this paper show that the derived variant ofSLC24A5, the largest effect pigmentation allele we know of, was segregating in these farmers. [Eastern farmer]This is not surprising. It was segregating in western farmers at high frequency as well. Among Caucasian hunter-gatherers, and even among hunter-gatherers from Mesolithic Sweden. It was, though, not so much found among Western European hunter-gatherers."

"Curiously, the authors mention that SLC45A2, another skin-lightening derived allele, which is much more concentrated in Europe, has been found segregating in Neolithic Aegeans. So it may be that the two major skin-lightening alleles were introduced by western and eastern farmers. Finally, the allele known to produce blue eyes in Europeans, found in high frequencies in Mesolithic European hunter-gatherers, was also found segregating in WC1. WC1 is the highest quality genome in their ancient data, so this seems a likely inference."

"What this tells us I think is that skin-lightening alleles have been segregating at appreciable frequencies for long time. They have a deep history. Periodically, a particular haplotype gets targeted for selection, and a sweep occurs. Personally, I am more and more leaning to the hypothesis that a diversity of functions and characteristics are the targets of this selection, with the phenotype often being a side effect. What is even more intriguing to me is that the peoples as distinct as Sardinians and Baloch don’t actually look that different physically. The great reflux even affected them, and with it perhaps came alleles which were selected upon and produced a relatively uniform phenotype from the Atlantic to the Indus?"

I believe that as well, I just can't figure out what precisely was going on.

Finally,

"Much of our genetic character is the product of cultural changes, rather than cultural changes being the product of our genetic character."

I believe what he's saying here is that innovation, technological innovation, creates a new culture, a new environment, and that new environment imposes selective pressure.

I'm not so sure that it doesn't work the other way around as well, however. If you're going to create a complicated culture you have to have communication skills, just as one example. At certain parts of human history that may have been impossible.

[ThirdTerm]

Ｉ looked into the thread started by bicicleur ("Early Neolithic genomes from the eastern Fertile Crescent") last week. But the thread was merged with "Tepe Hasanlu F38 belongs to R1b1a2a2-CTS1078/Z2103 ( Zagros - Iron Age )" in Ancient DNA studies. Elamite Iran's strong affinity to peoples in southern Pakistan is attributed to haplogroup G2b in the supplimentary part of the paper, which is well represented among the Kalash and Pashtun populations.

Y-chromosomal lineage determination

We determined Y-chromosome haplogroups in ancient male samples using clean_tree(85). This software implements SAMtools (86) mpileup to call alleles at given genomic coordinates (2,710 SNPs), which we obtained from ISOGG 2013 (International Society of Genetic Geneology). The number of SNPs identified in our samples are shown in Supplementary Table S10. It was not possible to determine the paternal lineage of AH2 due to insufficient number of reads. Derived alleles for F38 and WC1 can be found in Supplementary Table S11 and S12, respectively. WC1 belongs to haplogroup G2b. G2 Y-chromosomal haplogroups are more frequent in Turkey, southern Caucasus and Iran (87, 88). Furthermore, some populations from Pakistan and Southern Asia such as Kalash, Brahui and Pashtun also have the G haplogroup at a higher frequency than other populations (89, 90). The very unique G2b subclade is rarely represented around the world. G2b is mostly found in Pashtuns (91) and among Europeans mainly in Ashkenazi Jews (92). However, it is also found at very low numbers in some other regions in the Near East (87, 90, 93). G2b lineages have not yet been identified in ancient samples. The dominating G-derived lineage in the European Neolithic so far is G2a (3, 4). F38 belongs to sub-haplogroup R1b1a2a2-CTS1078/Z2103. This lineage can be included in the L23(xM412) clade, which is characterized by frequencies higher than 10% in the Caucasus, Turkey, Southeastern Europe, and Circum-Uralic populations, and is mostly found at very low frequencies in Western Europe. This pattern sharply contrasts with the distribution of M412-derived Y-chromosomes, which are very common in Western Europe but rare in the East (94). In ancient DNA studies, derived alleles that define the R1b1a2a2 lineage were found in five Yamnaya individuals and in two samples from the Poltkava culture (3, 17).

Although we observed two reads covering marker J2a1h1-M158, this is a C→T mutation and in addition, there are no upstream markers (ancestral alleles at J-M304, J2-M172 and J2a-M410) that would support including F38 in this lineage. In modern-day Iranian population, the most frequent Y-chromosome haplogroups are J2-M172 (22.5%) and J1-M267 (~10%), and the less frequent ones are R1a-M198 (0-25%) and R1b-M269 (95).

[Angela]

Thank you, Third Term, that's undoubtedly why I couldn't find it. The combined thread title doesn't refer to the title or author of the paper. I'll have to speak to Bicicleur and see if perhaps we should merge this one too.

[LeBrok]

"Much of our genetic character is the product of cultural changes, rather than cultural changes being the product of our genetic character."

I believe what he's saying here is that innovation, technological innovation, creates a new culture, a new environment, and that new environment imposes selective pressure.

I'm not so sure that it doesn't work the other way around as well, however. If you're going to create a complicated culture you have to have communication skills, just as one example. At certain parts of human history that may have been impossible.

Goes both ways. Nurture/culture and nature/DNA work together. Can't have one without the other. Can't develope milk drinking culture without LP gene, but LP gene can't make you drink milk. You can't have civilization without our big brains, and you can't have big brains if way of life/culture doesn't demand it. Like a positive reinforcement loop.

I merged both threads because people were posting same things in both. Unfortunately it merged with Y DNA them first, because it was started earlier.

[LeBrok]

Seems Dravidian could have been the language of Iranian Neolithic Farmers.

[Angela]

Goes both ways. Nurture/culture and nature/DNA work together. Can't have one without the other. Can't develope milk drinking culture without LP gene, but LP gene can't make you drink milk. You can't have civilization without our big brains, and you can't have big brains if way of life/culture doesn't demand it. Like a positive reinforcement loop.

I merged both threads because people were posting same things in both. Unfortunately it merged with Y DNA them first, because it was started earlier.

I agree; I think he's wrong about it going only in one direction. As for the merging, handle it however you think best; it'll be fine with me what ever you decide. I just thought I was going prematurely senile when I couldn't find it. :)

[Alan]

IMO the Elamites will be pretty much Iran_CHL or Iran_Neo like and show great affinity to Baloch as well other modern population of the Iranian_Plateau. However Baloch, though having the highest Iran_Neo affinity (~60-70%) have obviously non Iran_Neo ancestry connected to South Asia too.

The whole Sumerian_Elamite_ Harappa continuum will be predominantly Iran_Neo or Iran_CHL.

[Alan]

Seems Dravidian could have been the language of Iranian Neolithic Farmers.

Dravidian is a language that evolved in Indus Valley. Iran_Neolithic farmers are too old to be proto of anything. However what you probably mean is that Dravidian language evolved out of an Iran_Neo like people and Sumerian_Elamite_Dravidian have one origin and belong to the same language family. This of course is very plausible but still speculation. We still don't really know what language Sumerians and Elamites spoke. If the connection to Dravidian was so crystal clear I believe linguists would have found it already. So I don't know really.

[LeBrok]

Dravidian is a language that evolved in Indus Valley. Iran_Neolithic farmers are far too old to be proto of everything. However what you probably mean is that Dravidian language evolved out of an Iran_Neo like people and Sumerian_Elamite_Dravidian have one origin and belong to the same language family. This of course is very plausible but still speculation. We still don't really know what language Sumerians and Elamites spoke. If the connection to Dravidian was so crystal clear I believe linguists would have found it already. So I don't know really.

You are right on all counts. Just a speculation of Dravidian language family spread by Iran Neolithic folks.

[Sile]

Dravidian is a language that evolved in Indus Valley. Iran_Neolithic farmers are far too old to be proto of everything. However what you probably mean is that Dravidian language evolved out of an Iran_Neo like people and Sumerian_Elamite_Dravidian have one origin and belong to the same language family. This of course is very plausible but still speculation. We still don't really know what language Sumerians and Elamites spoke. If the connection to Dravidian was so crystal clear I believe linguists would have found it already. So I don't know really.

Elamite Dravidian

http://starling.rinet.ru/Texts/elam.pdf

https://www.academia.edu/7608175/Ela...mil_Connection

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4366740/

[Hauteville]

It's really interesting the plot of those ancient Genomes


And the modern genetic similarity with Balochi and Makrani

[bicicleur]

Thank you, Third Term, that's undoubtedly why I couldn't find it. The combined thread title doesn't refer to the title or author of the paper. I'll have to speak to Bicicleur and see if perhaps we should merge this one too.

My thread was allready merged with the Tepe Hasanlu thread.

[bicicleur]

Goes both ways. Nurture/culture and nature/DNA work together. Can't have one without the other. Can't develope milk drinking culture without LP gene, but LP gene can't make you drink milk. You can't have civilization without our big brains, and you can't have big brains if way of life/culture doesn't demand it. Like a positive reinforcement loop.

I merged both threads because people were posting same things in both. Unfortunately it merged with Y DNA them first, because it was started earlier.

the milk drinling gene probably existed long before dairy
only when dairy production started, the milk drinking gene got positively selected
same with white skin

[bicicleur]

the DNA sampled is more than 9000 years old
Sargon of Akkad is 2300 BC
there is a 5000 year gap between this sampled DNA and the Elamites, so dificult to draw conclusions
the Summerians didn't come from Zagros Mountains, but from central Mesopotamia (Samarra culture)
the Akkadians were Semitic E-M123, a subclade of the E-M35 Natufians