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Thread: Broushaki et al. "Early Neolithic genomes from the eastern Fertile Crescent"

  1. #401
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    Quote Originally Posted by rozenfeld View Post
    http://science.sciencemag.org/conten...cience.aaf7943

    Early Neolithic genomes from the eastern Fertile Crescent

    Farnaz Broushaki1, Mark G Thomas2, Vivian Link3,4, Saioa López2, Lucy van Dorp2, Karola Kirsanow1, Zuzana Hofmanová1, Yoan Diekmann2, Lara M. Cassidy5, David Díez-del-Molino2,6, Athanasios Kousathanas3,4,7, Christian Sell1, Harry K. Robson8, Rui Martiniano5, Jens Blöcher1, Amelie Scheu1,5, Susanne Kreutzer1, Ruth Bollongino1, Dean Bobo9, Hossein Davudi10, Olivia Munoz11, Mathias Currat12, Kamyar Abdi13, Fereidoun Biglari14, Oliver E. Craig8, Daniel G Bradley5, Stephen Shennan15, Krishna R Veeramah9, Marjan Mashkour16, Daniel Wegmann3,4,*,†, Garrett Hellenthal2,*,†, Joachim Burger1,*,†

    Science 14 Jul 2016:

    DOI: 10.1126/science.aaf7943

    Abstract

    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 pee-Neolithic population structure were preserved as farming spread into neighboring regions, and that the Zagros region was the cradle of eastward expansion.
    If it's true then the human history should be rewritten again. How on earth a relatively genetically close population separated 46-77,000 years ago when scientist estimated the Caucasoid race technically didn't even exist 40000 years ago only some basal Eurasian groups whom later became either Caucasoid or Mongoloid after separation.

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  3. #402
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    It's just getting more and more similar to the moderns, chr(1:9,20:21) 412K SNP

    Code:
            12 ancestral populations
        166770 total SNPs
         11400 flipped SNPs
          6935 heterozygous SNPs
             0 no-calls
         95569 absent SNPs
      0.426941 genotype rate
          mode genomewide
     
     95569 SNPs missing (no-call or absent)
     
     ----------------------------
     FINAL ADMIXTURE PROPORTIONS:
     ----------------------------
     
     28.71%  Gedrosia            
      0.00%  Siberian            
      0.26%  Northwest_African   
      0.00%  Southeast_Asian     
      8.76%  Atlantic_Med        
      5.71%  North_European      
      0.00%  South_Asian         
      0.00%  East_African        
     12.02%  Southwest_Asian     
      0.00%  East_Asian          
     44.53%  Caucasus            
      0.00%  Sub_Saharan
    Last edited by MfA; 07-25-2016 at 08:05 AM.
    E-M84>FGC18389>FGC18413>FGC18401>FGC18422>Y99171 tMRCA 2550ybp

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  5. #403
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    Quote Originally Posted by manus View Post
    If it's true then the human history should be rewritten again. How on earth a relatively genetically close population separated 46-77,000 years ago when scientist estimated the Caucasoid race technically didn't even exist 40000 years ago only some basal Eurasian groups whom later became either Caucasoid or Mongoloid after separation.
    Their separation times look inflated, ancient genome quality or assumed mutation rate has an effect. The same method they used obtained a more recent estimate time for West European and East Asian separation when used on modern genomes.

    More recently introduced methods, like MSMC, also give separation times that apparently contradict the numbers of this paper.

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  7. #404
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    Quote Originally Posted by MfA View Post
    It's just getting more and more similar to the moderns, chr(1:9,20:21) 412K SNP

    Code:
            12 ancestral populations
        166770 total SNPs
         11400 flipped SNPs
          6935 heterozygous SNPs
             0 no-calls
         95569 absent SNPs
      0.426941 genotype rate
          mode genomewide
     
     95569 SNPs missing (no-call or absent)
     
     ----------------------------
     FINAL ADMIXTURE PROPORTIONS:
     ----------------------------
     
     28.71%  Gedrosia            
      0.00%  Siberian            
      0.26%  Northwest_African   
      0.00%  Southeast_Asian     
      8.76%  Atlantic_Med        
      5.71%  North_European      
      0.00%  South_Asian         
      0.00%  East_African        
     12.02%  Southwest_Asian     
      0.00%  East_Asian          
     44.53%  Caucasus            
      0.00%  Sub_Saharan
    Quote Originally Posted by MfA View Post
    F38 which is between Iranians and Anatolians with slight southern shift. In fact It's where many Kurds should plot if they were included into the PCA.

    F38 study
    Appears that you were right!

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  9. #405
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    Full genome results, 675K SNP. Just uploaded to Gedmatch, M381564 should be available soon.

    F38 Hasanlu Iron Age, Iran. Dodecad K12b
    Code:
     28.81%  Gedrosia            
      0.00%  Siberian            
      0.12%  Northwest_African   
      0.00%  Southeast_Asian     
      7.63%  Atlantic_Med        
      4.44%  North_European      
      0.01%  South_Asian         
      0.00%  East_African        
     13.53%  Southwest_Asian     
      0.00%  East_Asian          
     45.46%  Caucasus            
      0.00%  Sub_Saharan 
    
    Single Population Sharing:
    
    #	Population (source)	Distance
    1	Kurds (Yunusbayev)	4.07
    2	Kurd (Dodecad)	5.47
    3	Iranian (Dodecad)	6.73
    4	Uzbekistan_Jews (Behar)	9.26
    5	Iranians (Behar)	9.28
    6	Azerbaijan_Jews (Behar)	12.24
    7	Assyrian (Dodecad)	12.95
    8	Georgia_Jews (Behar)	13.4
    9	Armenians_15 (Yunusbayev)	13.5
    10	Iranian_Jews (Behar)	13.68
    11	Turks (Behar)	14.36
    12	Armenian (Dodecad)	14.61
    13	Iraq_Jews (Behar)	16.01
    14	Turkish (Dodecad)	16.72
    15	Armenians (Behar)	17.86
    16	Kumyks (Yunusbayev)	19.57
    17	Lebanese (Behar)	20.39
    18	Turkmens (Yunusbayev)	20.99
    19	Druze (HGDP)	21.6
    20	Syrians (Behar)	22.57
    Last edited by MfA; 07-26-2016 at 06:55 PM.
    E-M84>FGC18389>FGC18413>FGC18401>FGC18422>Y99171 tMRCA 2550ybp

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  11. #406
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    Quote Originally Posted by MfA View Post
    Full genome results, 675K SNP. Just uploaded to Gedmatch, M122475 should be available soon.



    Code:
            12 ancestral populations
        166770 total SNPs
         18742 flipped SNPs
         11698 heterozygous SNPs
             0 no-calls
         50001 absent SNPs
      0.700180 genotype rate
          mode genomewide
     
     50001 SNPs missing (no-call or absent)
     
     
     ----------------------------
     FINAL ADMIXTURE PROPORTIONS:
     ----------------------------
     
     28.81%  Gedrosia            
      0.00%  Siberian            
      0.12%  Northwest_African   
      0.00%  Southeast_Asian     
      7.63%  Atlantic_Med        
      4.44%  North_European      
      0.01%  South_Asian         
      0.00%  East_African        
     13.53%  Southwest_Asian     
      0.00%  East_Asian          
     45.46%  Caucasus            
      0.00%  Sub_Saharan
    Updated cluster analysis, with some populations from the previous cluster analysis removed:



    And a MDS analysis:


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  13. #407
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    F38 Hasanlu, Iron Age Iran

    Eurogenes K13
    Code:
    North_Atlantic	2.81
    Baltic	2.82
    West_Med	10.58
    West_Asian	47.50
    East_Med	27.85
    Red_Sea	6.88
    South_Asian	1.56
    East_Asian	-    
    Siberian	-    
    Amerindian	-    
    Oceanian	-    
    Northeast_African	-    
    Sub-Saharan	-    
    
    Single Population Sharing:
    
    #	Population (source)	Distance
    1	Georgian	7.83
    2	Abhkasian	9.13
    3	Kurdish	9.7
    4	Armenian	10.19
    5	Georgian_Jewish	12.53
    6	Iranian	13.07
    7	Azeri	13.44
    8	Adygei	14.2
    9	Ossetian	15.07
    10	Kumyk	15.32
    11	Turkish	15.86
    12	North_Ossetian	16.35
    13	Balkar	16.48
    14	Assyrian	16.53
    15	Kabardin	18.04
    16	Kurdish_Jewish	19.58
    17	Chechen	19.75
    18	Lezgin	20.09
    19	Iranian_Jewish	20.16
    20	Tabassaran	22.9
    Eurogenes K15

    Code:
    North_Sea	5.63
    Atlantic	-    
    Baltic	-    
    Eastern_Euro	7.21
    West_Med	6.64
    West_Asian	42.44
    East_Med	30.16
    Red_Sea	6.45
    South_Asian	1.48
    Southeast_Asian	-    
    Siberian	-    
    Amerindian	-    
    Oceanian	-    
    Northeast_African	-    
    Sub-Saharan	-    
    
    Single Population Sharing:
    
    #	Population (source)	Distance
    1	Armenian	8.48
    2	Georgian_Jewish	10.03
    3	Kurdish	11.3
    4	Azeri	13.06
    5	Iranian	13.09
    6	Assyrian	14.29
    7	Turkish	14.41
    8	Georgian	14.83
    9	Kumyk	15.51
    10	Adygei	17.85
    11	Abhkasian	17.91
    12	Kurdish_Jewish	18.65
    13	Iranian_Jewish	18.91
    14	Lezgin	19.05
    15	Ossetian	19.23
    16	Balkar	19.93
    17	Kabardin	20.07
    18	Lebanese_Muslim	21.34
    19	North_Ossetian	21.35
    20	Tabassaran	21.7

    MDLP K13 Ultimate
    Code:
    Admix Results (sorted):
    
    #	Population	Percent
    1	Caucas-Gedrosia	40.04
    2	ANE	31.93
    3	NearEast	11.65
    4	ENF	10.61
    5	WHG-UHG	3.17
    6	ASI	2.27
    7	Arctic	0.34
    
    Single Population Sharing:
    
    #	Population (source)	Distance
    1	Kurd_WGA	4.44
    2	Kurd	5.05
    3	Baku_WGA	5.23
    4	Uzbekistani_Jew	6.9
    5	Azerbaijani	7.33
    6	Iranian	7.79
    7	Uzbek_WGA	7.8
    8	Azerbaijani_Dagestan	8.74
    9	Turk_Adana	10.89
    10	Georgian_Jews	10.95
    11	Georgian_Jew	11.02
    12	Azerbaijani_Jew	11.09
    13	Balkar	11.43
    14	Turk_Kayseri	11.55
    15	Iranian_Jew	11.69
    16	Kakheti	11.75
    17	Jew_Tat	11.9
    18	Kumyk	12
    19	Assyrian_WGA	12.18
    20	Kabardin	12.23
    MDLP K23b
    Code:
    Admix Results (sorted):
    
    #	Population	Percent
    1	Caucasian	41.15
    2	South_Central_Asian	30.04
    3	Near_East	12.51
    4	European_Early_Farmers	11.27
    5	Ancestral_Altaic	3.03
    6	North_African	0.99
    7	African_Pygmy	0.53
    8	Arctic	0.49
    
    Single Population Sharing:
    
    #	Population (source)	Distance
    1	Kurd ( )	7.84
    2	Kurd_North ( )	8.11
    3	Azeri ( )	9.63
    4	Kurd_East ( )	9.68
    5	Uzbek_Tashkent ( )	10.88
    6	Kurd_South ( )	11.08
    7	Baku_WGA ( )	11.18
    8	Uzbekistani_Jew ( )	11.44
    9	Turk_Adana ( )	13.26
    10	Iraqi_Chaldean ( )	13.38
    11	Azeri_Dagestan ( )	13.38
    12	Kurd_Jew ( )	13.61
    13	Assyrian_Iraqi ( )	13.71
    14	Iraqi_Mandean ( )	13.81
    15	Turk_Kayseri ( )	13.88
    16	Georgian_Jew ( )	14.24
    17	Iranian_Jew ( )	14.96
    18	Turk ( )	15.13
    19	Stalskoe_Kumyk ( )	15.35
    20	Tabassaran ( )	16.34
    HarappaWorld
    Code:
    Admix Results (sorted):
    
    #	Population	Percent
    1	Caucasian	47.6
    2	Baloch	29.17
    3	SW-Asian	13.43
    4	Mediterranean	6.66
    5	NE-Euro	3.01
    6	W-African	0.11
    7	Pygmy	0.03
    
    Single Population Sharing:
    
    #	Population (source)	Distance
    1	kurd (xing)	4.36
    2	kurd (yunusbayev)	4.4
    3	kurd (harappa)	7.61
    4	iranian (harappa)	8.38
    5	iranian (behar)	9.29
    6	uzbekistan-jew (behar)	9.33
    7	assyrian (harappa)	10.71
    8	armenian (harappa)	11.04
    9	azeri (harappa)	11.57
    10	turkish (harappa)	11.74
    11	iraqi-mandaean (harappa)	11.92
    12	azerbaijan-jew (behar)	12.63
    13	iranian-jew (behar)	12.67
    14	armenian (yunusbayev)	13.3
    15	georgia-jew (behar)	14.04
    16	armenian (behar)	14.49
    17	iraq-jew (behar)	14.72
    18	turk (behar)	14.77
    19	turk-kayseri (hodoglugil)	15.08
    20	iraqi-arab (harappa)	15.83
    Last edited by MfA; 07-26-2016 at 09:14 AM.
    E-M84>FGC18389>FGC18413>FGC18401>FGC18422>Y99171 tMRCA 2550ybp

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  15. #408
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    significant red sea in eurogenes k13 6.88%
    i score 7%
    i bet he would score arab/egyption in dna land
    very cool results
    i am not expert like you guys but result look like kurds and it is in kurdish area no ?
    regards
    adam

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  17. #409
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    Quote Originally Posted by Ryukendo View Post
    Immchr, just because Steppe LMBA contribution to Iranians was not explicitly covered in the paper does not mean that it does not exist, or that it is not easily inferred from the PCAs from David or the qpAdms in the supplementary models; furthermore Kurd using qpAdm has already shown that Iranians are basically a 2-way mix between Iran_Chalcolithic and 25% Andronovo/Sintashta-like populations.

    Wealth among Rg Vedic Aryans is primarily defined in terms of cattle and herds, and not in terms of grain, in common with Dinka and Nuer and Bedouin and in contrast to settled agricultural societies. The sanskrit word for war, 'Gavisti', literally means cattle-desire, and testifies to the central role of cattle raiding in their society, in common with other peoples for whom a pastoral economy was prominent. As for the Mahabharata, this was in the proto-historic period already when they had esconced themselves as an elite in India, so its natural that they would look down on their poorer counterparts in the North despite common origin, just like the Nahua-Chichimec phenomenon.

    I feel like your positions are constantly slipping and sliding around the evidence, instead of incorporating them. It seems like any possible movement from India to Europe in any timeframe can be associated with IE in your mind, whether it took place before Yamnaya, or during Yamnaya, or in the Yamnaya-Andronovo transition, or even during the movement of Iran_N or CHG populations out of India into the Middle East and the Caucasus in the Paleolithic. In any case, you seem to have accepted that, despite possible movements from Iran to Yamnaya or Andronovo, Yamnaya-like input or Andronovo-like input into South Asians is still necessary to explain their current ancestry; which means that the overall movement must have entered into the Steppe and Eastern Europe before plunging back to India via Yamnaya, so no getting around the fact that a Europe-->India movement is required either way, and a proximate source of genetic ancestry from the East European steppes is a necessary source for basically all Indo-European populations, as opposed to a spread from Iran bidirectionally only.
    1) Was there really a movement of Iran_N or CHG populations out of India into the Middle East and the Caucasus in the Paleolithic? I thought that Iran N or CHG migrated to India from the Zagros.

    2) Was there really possible movements from Iran to Yamnaya or Andronovo? If so when and whom?
    Thank you

  18. #410
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    Quote Originally Posted by Hando View Post
    1) Was there really a movement of Iran_N or CHG populations out of India into the Middle East and the Caucasus in the Paleolithic? I thought that Iran N or CHG migrated to India from the Zagros.

    2) Was there really possible movements from Iran to Yamnaya or Andronovo? If so when and whom?
    Thank you
    No there isn't, I don't think there is any sign of either, its just something that Immchr likes to postulate.

    As it is, the transition from Iran_Hotu to Iran_N sees a shift away from ENA/Onge and maybe some weird Central Asian thing towards more West Eurasian ancestry and more basal, so if anything the evidence points towards Iran_N emerging from west of its sampled position, and not Megargh like Immchr suggests.

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