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Thread: An Ancient Harappan Genome Lacks Ancestry from Steppe Pastoralists or Iranian Farmers

  1. #891
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    Quote Originally Posted by Aleph View Post
    ...

    "The admix dates even for all the Inpe samples are ALL well after the Neolithic"
    Do you happen to have these dates?
    "admixture between Iranian farmer–related and
    AHG-related ancestry in the outliers is several
    millennia before the time they lived (71 15
    generations, corresponding to a 95% confidence
    interval of ~5400 to 3700 BCE assuming 28 years
    per generation) (13, 47). Thus, AHG- and Iranian
    farmer–related groups were in contact well before
    the time of the mature IVC at ~2600 to 1900 BCE"

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     Aleph (11-10-2019)

  3. #892
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    Why does Aigyrzhal_BA I11526 of Kyrgyzstan have the Indian Subcontinent-specific mtdna R6a2?

    It is mentioned in this paper
    https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3968120/
    All the Mauritian coding region sequences (GenBank accession numbers: KJ411336-KJ411423) could be assigned to 72 haplogroups and subhaplogroups (Table S3). However, to accomplish this affiliation, the complete mtDNA genome sequencing of nine samples (Figure S1) was necessary (GenBank accession numbers: KC577353-KC577361). Sample Ma-82 belongs to M5b haplogroup (with the 8784T defining mutation), samples Ma-70 and Ma-79 belong to the H13a2a haplogroup (sharing the 709, 1008, 2259 and 14872 diagnostic transitions), sample Ma-84 to the D4a subhaplogroup (sharing 152 3206 8473 14979 16129 diagnostic motif) and sample Ma-44, although it does not have the 16189 mutation, is classified as B4'5 as it has 8281–8289del. Some of these sequences have allowed us to define new subhaplogroups. Sample Ma-46 is classified as M42 (9156). This sequence defines a new branch of M42 [22], named M42b2 (Figure S2), and characterized by 1053 4197 15241 15562 and 16278 mutations. Sample Ma-66 is classified as R6 (Figure S3). This sequence redefines R6a1b subhaplogroup (12133 15067 16266!) and its sub-branches R6a1b1 (5894 16213) and R6a1b1a (15100), and also redefines the branch R6a1 (228 11075 14058 16274!), R6a1a (6305 8584 8650 16318 16320) and its sub-branch R6a1a1 (195! 373 961 7316). We also defined a new branch R6a2 (7202 9449 14470 16172). Ma-19 belongs to M49 haplogroup as it has 3780 and 16234 mutations; however, its further classification into subsequent clades remained unclear because it has the 10514 mutation in common with M49c, and the 11542 with M49d, but no other defining mutations for any subhaplogroup. Finally, sample Ma-12 is classified as M* as it does not share any subhaplogroup defining mutation.

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  5. #893
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    Quote Originally Posted by client View Post
    Why does Aigyrzhal_BA I11526 of Kyrgyzstan have the Indian Subcontinent-specific mtdna R6a2?

    It is mentioned in this paper
    https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3968120/
    I noticed that too. They also weirdly fit roughly on the SA cline but this sample seems to have minor IVC ancestry, and distantly related with modern Kalash.


    Target: KGZ_Aigyrzhal_BA:I11526
    Distance: 1.9900% / 0.01990047
    Aggregated
    37.2 TKM_Geoksyur_En
    15.2 RUS_Afanasievo
    13.8 RUS_Tyumen_HG
    13.0 KAZ_Dali_EBA
    12.8 IRN_Shahr_I_Sokhta_BA2
    8.0 TJK_Sarazm_En


    The other one has more

    Target: KGZ_Aigyrzhal_BA:I11527
    Distance: 1.5295% / 0.01529522
    Aggregated
    41.6 TKM_Geoksyur_En
    26.8 KAZ_Dali_EBA
    16.2 RUS_Afanasievo
    15.0 IRN_Shahr_I_Sokhta_BA2
    0.4 RUS_Tyumen_HG
    Last edited by pegasus; 11-11-2019 at 06:49 AM.

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  7. #894
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    Very interesting, I was willing to dismiss the Onge here as noise, but I guess it's real. Translate close enough in amount to the SIS2 above.

    Aigyrzhal_BA
    "Sarazm_N" 52.15
    "Kumsay_EBA" 33.5
    "Poltavka" 10.2
    "Onge.DG" 3.4
    "Malawi_Hora_Holocene" 0.4
    "Mota" 0.3
    "Yamnaya_Kazakhstan" 0.05
    "distance%=0.2334 / distance=0.002334"
    Columns: ,Barcin_N,Levant_N,Iran_N,CHG,Taforalt,MA1,Sunghir ,Brazil_Sumidouro_10100BP,EHG,IGHG_Serbia,Afanasie vo,Baikal_EN,Devils_Gate_N,Nepal_ancient,Vanuatu_a ncient,Ust_Ishim
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  9. #895
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    Quote Originally Posted by Kale View Post
    Very interesting, I was willing to dismiss the Onge here as noise, but I guess it's real. Translate close enough in amount to the SIS2 above.

    Aigyrzhal_BA
    "Sarazm_N" 52.15
    "Kumsay_EBA" 33.5
    "Poltavka" 10.2
    "Onge.DG" 3.4
    "Malawi_Hora_Holocene" 0.4
    "Mota" 0.3
    "Yamnaya_Kazakhstan" 0.05
    "distance%=0.2334 / distance=0.002334"
    Columns: ,Barcin_N,Levant_N,Iran_N,CHG,Taforalt,MA1,Sunghir ,Brazil_Sumidouro_10100BP,EHG,IGHG_Serbia,Afanasie vo,Baikal_EN,Devils_Gate_N,Nepal_ancient,Vanuatu_a ncient,Ust_Ishim

    Gonur outlier and Aigryzhal seem to be part of some mysterious population

    Target: TKM_Gonur1_BA_o:I1783
    Distance: 1.9553% / 0.01955267
    Aggregated
    45.0 TKM_Geoksyur_En
    24.6 RUS_Tyumen_HG
    17.8 RUS_Afanasievo
    12.6 IRN_Shahr_I_Sokhta_BA2

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  11. #896
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    Quote Originally Posted by Kale View Post
    Very interesting, I was willing to dismiss the Onge here as noise, but I guess it's real. Translate close enough in amount to the SIS2 above.

    Aigyrzhal_BA
    "Sarazm_N" 52.15
    "Kumsay_EBA" 33.5
    "Poltavka" 10.2
    "Onge.DG" 3.4
    "Malawi_Hora_Holocene" 0.4
    "Mota" 0.3
    "Yamnaya_Kazakhstan" 0.05
    "distance%=0.2334 / distance=0.002334"
    Columns: ,Barcin_N,Levant_N,Iran_N,CHG,Taforalt,MA1,Sunghir ,Brazil_Sumidouro_10100BP,EHG,IGHG_Serbia,Afanasie vo,Baikal_EN,Devils_Gate_N,Nepal_ancient,Vanuatu_a ncient,Ust_Ishim
    Try using DMXX's simulated AASI_NW to see if that works better. And if it works well, then use it alongside with Onge, there would probably be no Onge left in that case.

  12. #897
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    I have used the oldest Afanasievo sample


    Target: IRN_Shahr_I_Sokhta_BA1:I11476
    Distance: 2.6519% / 0.02651930
    83.4 IRN_Tepe_Hissar_C
    10.0 RUS_Afanasievo:I5270
    6.6 IRN_Ganj_Dareh_N
    0.0 IRN_Shahr_I_Sokhta_BA2
    0.0 TJK_Sarazm_En

    IRN_Shahr_I_Sokhta_BA1:I11476 is dated to ~4600years ago

    with avg
    Target: IRN_Shahr_I_Sokhta_BA1:I11476
    Distance: 2.7628% / 0.02762834
    84.6 IRN_Tepe_Hissar_C
    9.4 RUS_Afanasievo
    5.6 IRN_Ganj_Dareh_N
    0.4 IRN_Shahr_I_Sokhta_BA2
    0.0 TJK_Sarazm_En

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  14. #898
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    Quote Originally Posted by Aleph View Post
    Try using DMXX's simulated AASI_NW to see if that works better. And if it works well, then use it alongside with Onge, there would probably be no Onge left in that case.
    I'm using F3 outgroup not G25 for nmonte.
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  16. #899
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    Quote Originally Posted by client View Post
    I have used the oldest Afanasievo sample


    Target: IRN_Shahr_I_Sokhta_BA1:I11476
    Distance: 2.6519% / 0.02651930
    83.4 IRN_Tepe_Hissar_C
    10.0 RUS_Afanasievo:I5270
    6.6 IRN_Ganj_Dareh_N
    0.0 IRN_Shahr_I_Sokhta_BA2
    0.0 TJK_Sarazm_En

    IRN_Shahr_I_Sokhta_BA1:I11476 is dated to ~4600years ago

    with avg
    Target: IRN_Shahr_I_Sokhta_BA1:I11476
    Distance: 2.7628% / 0.02762834
    84.6 IRN_Tepe_Hissar_C
    9.4 RUS_Afanasievo
    5.6 IRN_Ganj_Dareh_N
    0.4 IRN_Shahr_I_Sokhta_BA2
    0.0 TJK_Sarazm_En
    Could this explain the minor presence of R1b in south Asia? I guess that would depend on the specific subclades of south Asian R1b (don't know a lot of details regarding this), if they are more recent then they might have been brought by MLBA instead.

  17. #900
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    Quote Originally Posted by client View Post
    Maybe we're dealing with different kinds of "AASI" or "AHG" here.


    Interesting



    What was the height of the lone female specimen that was analysed? ...
    Not the genome tested one, but one in the reconstruction.
    "7.2 A1 BR02 is a male of 16–18 years of age & height 177.28 3.24 centimeters.
    7.2 A2 BR36 is a female of 36–50 years & height 167.07 4.25 Centimeters"

    A2 BR36 (top)



    "at Rakhigarhi cemetery, the brick-lined burials were among the most elaborately constructed graves, implying a high social or ritual status for the deceased ... We note that every individual discovered in a brick-lined burial was likely, by anthropological examination, to have been female. Therefore, if we accept the hypothesis that the people buried in the brick-lined graves actually belonged to the dominant group in Rakhigarhi society, we must reconsider the social role of some Harappan females at that time."
    Last edited by parasar; 11-19-2019 at 05:16 PM.

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