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Thread: Mammoth Paper from Qiaomei Fu's group on Genetic history of East Asia

  1. #21
    Quote Originally Posted by Ryukendo View Post
    This is incredibly, incredibly disappointing... Those of us who are interested in the ethnogenesis of Sinitic-speakers have effectively no recourse except to take their claim based on the autosomal results ("Han originating in Yellow River Valley") at face value.

    Its very noticeable that the modern Han are shifted in the direction of the Oakaie1 genomes when compared to early coastal Northern Chinese agriculturalists (which could come either from Wuzhuanggouliang --> Coastal Northern China and then Southern China <--> Northern China, or a single movement Oakaie1 --> Coastal Northern China, interesting either way), and from the earlier studies from Jilin University ~2014 we get early Northeast Asian agriculturalists being all Y-chromosome haplogroup N. To get anywhere we need corroboration of these earlier results...

    Ah well, first thing to do is probably to analyse Wuzhuanggouliang and these Coastal Northeast China samples together, there could still be differences as Wuzhuanggouliang ended up projected among Tu and Tibetan while these end up among Daur and Xibo.
    Dr. Fu explained things clearly in the public record, and it's preferable to concentrate on understanding the conclusions of the authors based on the scientific method and not take a detour to speculative ideas. We don't want to turn the discussion of East Asian ancestry into another back-and-forth between bloggers jousting their pet theories ad nauseam.

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  3. #22
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    Quote Originally Posted by Ryukendo View Post
    This is incredibly, incredibly disappointing... Those of us who are interested in the ethnogenesis of Sinitic-speakers have effectively no recourse except to take their claim based on the autosomal results ("Han originating in Yellow River Valley") at face value.
    Those were my first thoughts as well. Perhaps the topic is just too sensitive? Compare with the relatively frank, data-driven treatment that Austronesian origins receive further on in the paper. I'm getting the feeling that researchers are self-censoring "just to be on the safe side", as it were, because they don't know where the red lines lie.
    Last edited by Inigo Montoya; 05-15-2020 at 09:05 PM.

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  5. #23
    Quote Originally Posted by Inigo Montoya View Post
    Those were my first thoughts as well. Perhaps the topic is just too sensitive? Compare with the relatively frank, data-driven treatment that Austronesian origins receive further on in the paper. I'm getting the feeling that researchers are self-censoring "just to be on the safe side", as it were, because they don't know where the red lines lie.
    You are welcome to ask the authors about the YDNA data without resorting to needless speculation.

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  7. #24
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    Quote Originally Posted by Inigo Montoya View Post
    Those were my first thoughts as well. Perhaps the topic is just too sensitive? Compare with the relatively frank, data-driven treatment that Austronesian origins receive further on in the paper. I'm getting the feeling that researchers are self-censoring "just to be on the safe side", as it were, because they don't know where the red lines lie.
    While its disappointing this is very speculative, I agree with Talljimmy. Maybe the Y-chromosomes were poorly covered or contaminated (the Y must surely have been captured because if the same methodology as the Leipzig and Reich labs was used then the Y chromosome is covered.)

    Someone could send some emails and check.
    Quoted from this Forum:

    "Which superman haplogroup is the toughest - R1a or R1b? And which SNP mutation spoke Indo-European first? There's only one way for us to find out ... fight!"

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  9. #25
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    Could be they mean to make the uniparentals a separate paper.

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  11. #26
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    Well, usually papers with uniparental markers are published before papers with autosomal analysis. It's still weird, but OK, time will tell. I hope two other papers about East Asian ancient DNA(the ones which preprints were posted recently) would be published as soon as possible.

    UPD: Also, why still no proper(autosomal) ancient DNA from Korea? Is their climate/soil that destructive for DNA?

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  15. #28
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    Y chr Haplogroup Assignments:

    XJS1309_M4 Xiaojingshan N1b1:F4201 (~N-F2905)
    BS Boshan N1b1:F4201 (~N-F2905)
    L5696_d Tanshishan O1b1a1a1a:F1252 (~O-F1252)
    L5701_d Xitoucun O2a1:F573 (~O-L465) LowCoverage
    L7415 Tanshishan O1a2:M50 (~O-M110)
    LD1 Liangdao1 O1a (~O-M119)
    I3612 Taiwan_Hanben O2a2b2a2b (~O-F706)
    I3733 Taiwan_Hanben O1a1a1a1 (~O-F78)
    I3736 Taiwan_Hanben O1a1a1a1 (~O-F78)
    I3614 Taiwan_Hanben O2a2b2b1 (~O-Y125645)
    I3618 Taiwan_Hanben O2a2b2a2b (~O-F706)
    I3731 Taiwan_Hanben O1a1a1a1 (~O-F78)
    I3734 Taiwan_Hanben O2a2a1a2a2 (~O-Y26395)
    I14934 Taiwan_Hanben O1a1a1a1 (~O-F78)
    I8080 Taiwan_Hanben O1a1a1a (~O-F140)
    I8081 Taiwan_Hanben O1a1a1a (~O-F140)
    I13695 Taiwan_Hanben O1a1a1a (~O-F140)

    I used published genotype files to make these assignments.
    List of positive and negative calls for each sample.
    Last edited by kolgeh; 05-16-2020 at 12:06 PM.

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  17. #29
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    Interesting...

    CHN_Bianbian_N:Bianbian BCE:7562
    CHN_Xiaogao_N:Xiaogao BCE:6734
    CHN_Qihe_N:Qihe2_d BCE:6443
    CHN_Yumin_N:Yumin BCE:6425
    CHN_Liangdao1_N:LD1 BCE:6240
    CHN_Boshan_N:BS BCE:6230
    CHN_Xiaojingshan_N:XJS1311_M16 BCE:5910
    CHN_Xiaojingshan_N:XJS1309_M4 BCE:5856
    CHN_Xiaojingshan_N:XJS1309_M7 BCE:5846
    CHN_Liangdao2_N:LD2 BCE:5625
    CHN_Xitoucun_N:L5700 BCE:2492
    CHN_Xitoucun_N:L5705 BCE:2492
    CHN_Tanshishan_N:L7415 BCE:2425
    CHN_Chuanyun_Historic:L5694 CE:1642

    Code:
    Distance to:    CHN_Yumin_N:Yumin
    0.05823815    Oroqen
    
    Distance to:    CHN_Xitoucun_N:L5705
    0.04533049    Atayal
    
    Distance to:    CHN_Xitoucun_N:L5700
    0.04627053    Kinh_Vietnam
    
    Distance to:    CHN_Xiaojingshan_N:XJS1311_M16
    0.03164072    Korean
    
    Distance to:    CHN_Xiaojingshan_N:XJS1309_M7
    0.06490223    Mongola
    
    Distance to:    CHN_Xiaojingshan_N:XJS1309_M4
    0.03990579    Mongola
    
    Distance to:    CHN_Xiaogao_N:Xiaogao
    0.04376662    Xibo
    
    Distance to:    CHN_Tanshishan_N:L7415
    0.03985199    Atayal
    
    Distance to:    CHN_Qihe_N:Qihe2_d
    0.05251533    Thai
    
    Distance to:    CHN_Liangdao2_N:LD2
    0.05120589    Vizayan
    
    Distance to:    CHN_Liangdao1_N:LD1
    0.05216001    Vizayan
    
    Distance to:    CHN_Chuanyun_Historic:L5694
    0.02823362    Han_Hubei
    
    Distance to:    CHN_Boshan_N:BS
    0.03490705    Mongola
    
    Distance to:    CHN_Bianbian_N:Bianbian
    0.03952560    Korean
    Last edited by Ajeje Brazorf; 05-16-2020 at 07:49 PM.

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  19. #30
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    Quote Originally Posted by Ebizur View Post
    The oldest specimen from southern China tested in this study should be the specimen from Qihe, "Qihe2":

    In the PCA graph, the Qihe specimen appears at the southern end of present-day Han Chinese variation. It does not cluster with present-day Austronesian, Kra-Dai, or Austroasiatic samples, with whom one might expect it to cluster under the hypothesis that pre-Qin/Han inhabitants of what is now southern China (including Fujian) were speakers of Austronesian, Kra-Dai, or Austroasiatic languages.

    On the other hand, the Tanshishan and Xitoucun specimens from several thousand years later and somewhat northeast of Qihe Cave within Fujian Province do cluster with the earlier (Liangdao) and contemporary (Suogang) samples from islands in the Taiwan Strait. These samples appear intermediate between the ancient Qihe2 specimen and the southern end of present-day Han Chinese variation on one side and present-day Austronesian-speaking aboriginal inhabitants of the island of Taiwan on the other.
    The Qihe (red circle) and Chuanyan (red diamond) samples are from inland southern Fujian. Chuanyan falls roughly where we'd expect modern-day Fujianese and Taiwanese to be on a PCA cline, which makes sense since that sample is from only 300-400 years ago, and should be broadly representative of the Qing-era South Chinese colonists in Taiwan.



    The other southern samples are from coastal Fujian and the Taiwan strait.
    Last edited by okarinaofsteiner; 05-16-2020 at 07:38 PM.

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