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Thread: The deep population history of northern East Asia from the Late Pleistocene to the

  1. #11
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    Quote Originally Posted by thejkhan View Post
    Are these the oldest C2 and oldest D (assuming the DE is D) samples to date?



    Would be interesting to find out where it fits in the P tree. Could be a Q as well.
    Definitely seems like it! Hopefully the samples have good coverage and can be analyzed.
    Y-DNA: R1b-U152 > L2 > Z367 > Z34 > Z33 > BY164497> BY3604 > FT190670 (Réveillon, Orne, France)

    mtDNA: X2 (probably X2m1) Calabria, Italy

    Maternal Y-DNA: J2a-M67 > Z1847 > Y4036 > Z467 > Z447> L210 (Calabria, Italy)

    Paternal mtDNA: K1b2b (France)

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  3. #12
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    Quote Originally Posted by Shuzam87 View Post
    NE20 F AR33K AR33K 34,324–32,360CalBP B –
    NE56 M AR19K AR19K 19,587–19,175CalBP G2 C2
    NE34 M AR14.5K AR14K 14,932–14,176CalBP D4h3 C
    NE-5 M AR14.1K AR14K 14,814–14,017CalBP [email protected] C
    NE-1 F AR12K AR13-10K 12,735–12,486CalBP D4g –
    NE-8 M AR11K AR13-10K 11,601–11,176CalBP D4o DE
    NE57f M AR11K_deleted– 11,206–10,765CalBP – –
    NE36f U AR10.6K_deleted– 11,065–10,513CalBP D4h4 –
    NE-3 M AR10.6K AR13-10K 10,996–10,429CalBP M8 C
    NE-4 M AR10.5K AR13-10K 10,740–10,302CalBP M8 C
    NE30g M AR9.9K_2d.rel.AR10.5K_deleted- 10,167–9,676CalBP D4m C
    NE45 M AR9.2K_o AR9.2K_o 9,425–9,029CalBP G1a1a P
    NE44f M AR9.2K_deleted – 9,425–9,027CalBP D4c1 –
    NE35 F AR8.9K ARpost9K 9,131–8,770CalBP R11 –
    NE-16 F AR8.5K ARpost9K 8,723–8,421CalBP D4o –
    NE49 F AR8.3K ARpost9K 8,425–8,204CalBP D4o –
    NE39 M AR8.1K ARpost9K 8,340–8,029CalBP D4m2 C
    NE58h M AR7.3K_LowCov – 7,425–7,168CalBP D4e5 –
    NE-18f M AR7K_deleted– 7,245–6,894CalBP D4h3 –
    NE19 M AR7K ARpost9K 7,167–6,854CalBP [email protected] C
    NE29 F AR6.87K ARpost9K 6,993–6,747CalBP D4c1 –
    NE-22 M AR6.84K ARpost9K 6,986–6,676CalBP D4m C
    NE-9 F AR6.33K ARpost9K 6,440–6,205CalBP C4a1a+195
    NE-2 M AR6.32K ARpost9K 6,437–6,201CalBP D4m C
    NE61h U AR3.4K_LowCov – 3,485–3,360CalBP D4b1a2a –
    What really stands out in these Y-haplogroup assignments is the utter lack of Haplogroup N-M231, which is very prevalent in North Eurasia today. This goes to show that modern-day haplogroup distributions are not always reliable in trying to infer their ancient histories. I'm guessing N-M231-carrying men were residing further south in the Pleistocene.
    Last edited by alchemist223; 05-27-2021 at 08:45 PM.
    Y-DNA: R1b-U152 > L2 > Z367 > Z34 > Z33 > BY164497> BY3604 > FT190670 (Réveillon, Orne, France)

    mtDNA: X2 (probably X2m1) Calabria, Italy

    Maternal Y-DNA: J2a-M67 > Z1847 > Y4036 > Z467 > Z447> L210 (Calabria, Italy)

    Paternal mtDNA: K1b2b (France)

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  5. #13
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    No sooner had I pined for a Fu-led East Asian study than she delivered exactly that in spades! The Amur River Basin must be one of the most well-covered regions at this point. I hope she can follow this up with a similar transect from further south.
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  7. #14
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    NE45 seems to be at least Q from the bam, maybe Q1a even
     
    haplogroup marker_name mutation reads state
    F L470 A->T 3 D
    F F1320 G->A 1 D
    F P163 A->T 1 D
    F CTS4443 A->T 2 D
    F P135 C->T 1 D
    F P160 A->C 1 D
    F P158 C->T 8 D
    F2 M427 G->A 1 A
    Freq. Mut. SNP in R L147 T->C 1 A
    Freq. Mut. SNP in R L128 T->C 44 D
    IJK L16 G->A 1 D
    K2 M526 A->C 1 D
    P1 or K2b2a CTS3446 C->A 1 D
    P1 or K2b2a CTS10081 C->A 1 D
    P1 or K2b2a CTS10085 A->G 3 D
    P1 or K2b2a M1263 C->T 2 D
    P1 or K2b2a PF5867 G->A 1 D
    P1 or K2b2a CTS196 C->T 1 D
    P1 or K2b2a CTS9162 C->T 4 D
    P1 or K2b2a CTS7481 C->T 1 D
    P1~ or K2b2a~ L471 A->G 1 D
    P1~ or K2b2a~ L268 A->G 1 D
    Q L232 G->A 1 D
    Q FGC1755 C->T 1 D
    Q F1829 T->C 1 D
    Q1 CTS4793 C->G 1 D
    Q1a F3489 C->G 1 D
    Q1a1a1b1~ PH1003 C->T 1 A
    Q1a1b Z36017 T->C 1 A
    Q1a1b YP1470 T->C 1 A
    Q1a1b Z36026 A->G 1 A
    Q1a1b Z36035 T->C 1 A
    Q1a1b Z36018 A->T 2 A
    Q1a1b Z36013 G->C 1 A
    Q1a2 F5169 T->C 2 A
    Q1a2a~ F4775 G->A 1 A
    Q1a2a1~ YP799 C->T 2 A
    Q1a2a1~ YP851 C->T 1 A
    Q1a2a1~ YP835 C->T 1 A
    Q1a2a1a4b~ YP1680 A->G 1 A
    Q1a2a2a~ Y17232 C->A 3 A
    Q1a2a2a~ YP4385 G->A 1 A
    Q1a2a2a~ YP4389 G->A 1 A
    Q1a2a2b~ F4833 G->T 3 A
    Q1b CTS7714 T->G 2 A
    Q1b M1156 A->G 1 A
    Q1b L56 G->A 3 A
    Q1b1~ M1037 G->A 1 A
    Q1b1~ CTS10434 G->A 1 A
    Q1b1~ M1141 C->T 3 A
    Q1b1a1a CTS11663 C->A 1 A
    Q1b1a1a1e1a~ L767 G->C 1 A
    Q1b1a1a1e1a1 CTS479 G->C 2 A
    Q1b1a1a1e1c~ Y11653 G->A 10 A
    Q1b1a1a1e2 Y12423 G->A 3 A
    Q1b1a1a1e3~ SK1973 A->G 1 A
    Q1b1a1a1h1 Z19460 C->T 1 A
    Q1b1a1a1i Z19295 C->G 1 A
    Q1b1a1a1i1 Z19318 T->C 2 A
    Q1b1a1a1i1a1a Z19340 A->G 3 A
    Q1b1a1a1i1a1a Z19350 A->G 1 A
    Q1b1a1a1i1a1a1~ Z35897 C->T 4 A
    Q1b1a1a1j Z19363 G->C 1 A
    Q1b1a1a1j Y779 T->C 1 A
    Q1b1a1a1l SK281 G->C 1 A
    Q1b1a1a1m2b~ Y26467 T->C 1 A
    Q1b1a1a1p Z35555 G->A 1 A
    Q1b1a1a1u~ Z35750 C->T 1 A
    Q1b1a1a1v~ BZ3493 C->A 6 A
    Q1b1a1a1v~ BZ3494 C->T 1 A
    Q1b1a1b~ BY1535 A->G 1 A
    Q1b1a1b~ Y7342 G->A 1 A
    Q1b1a1b~ Y7330 C->A 1 A
    Q1b1a1b1a2~ Y18222 T->G 1 A
    Q1b1a2~ M1049 G->C 1 A
    Q1b1a2a~ Z19278 C->G 1 A
    Q1b1a2a1a1a3~ BZ2617 G->C 2 A
    Q1b1a2a1b Y2830 G->A 1 A
    Q1b1a2a1b CTS705 C->T 1 D
    Q1b1a2a2 YP911 C->G 1 A
    Q1b1a2a3a1a~ FGC12198 G->A 1 A
    Q1b1a2a3a1a~ FGC12219 G->A 1 A
    Q1b1a3 Y5228 G->A 1 A
    Q1b1a3a1~ YP783 C->T 1 A
    Q1b1a3b Y12451 G->A 1 A
    Q1b1a3b1a1~ Z35987 G->A 1 A
    Q1b1b~ YP4072 G->A 1 A
    Q1b2a F4674 C->T 1 A
    Q1b2b1~ FGC6976 C->T 1 A
    Q1b2b1~ FGC6974 T->A 1 A
    Q1b2b1a1a~ Y15693 T->A 1 A
    Q1b2b1a1a~ Y17794 A->G 1 A
    Q1b2b1b1~ CTS4794.2 C->A 1 A
    Q1b2b1b2~ BZ1498 C->T 7 A
    Q1b2b1b2b1~ M323.1 C->T 2 A
    Q2 F3084 A->C 1 A
    Q2 F1406 A->G 2 A
    Q2 Y1047 C->T 1 A
    Q2 F2532 T->C 2 A
    Q2 Y1118 T->G 1 A
    Q2 Y1040 C->T 1 A
    Q2 F2250 G->A 1 A
    Q2 F1974 G->A 4 A
    Q2 F1280 C->A 1 A
    Q2 Y1101 G->A 1 A
    Q2 Y1052 G->A 3 A
    Q2a FGC1877 C->T 3 A
    Q2a F2230 G->A 5 A
    Q2a F1349 T->A 2 A
    Q2a1 FGC1875 G->T 2 A
    Q2a1a FGC1840 C->G 1 A
    Q2a1a FGC1832 G->A 1 A
    Q2a1a FGC1806 C->T 6 A
    Q2a1a1a1 FGC1912 G->A 3 A
    Q2a1a1a1 FGC1919 C->T 1 A
    Q2a1a1a1a1a FGC1932 A->G 1 A
    Q2a1a1a1a1a2a2a~ L315 C->T 1 A
    Q2a1a1a5a~ A12479 C->G 1 A
    Q2a1a2a YP1095 T->G 1 A
    Q2a1a2a1a1a YP1237 C->T 2 A
    Q2a1a2a3a~ BZ228 C->T 1 A
    Q2a1a2b2a1~ BZ260 T->C 1 A
    Q2a1a2b2a3~ Y86770 A->G 1 A
    Q2a1a2c1a Y23607 G->C 1 A
    Q2a1a2c1a1 BZ3077 A->T 1 A
    Q2a1a2c2~ Y88251 G->A 1 A
    Q2a1a2c2~ Y87218 T->G 1 A
    Q2a1a3 BZ319 A->C 1 A
    Q2a1a3a1 BZ3057 C->G 1 A
    Q2a1a3a1a~ BZ3064 C->T 1 A
    Q2a1a3a2~ BZ323 G->A 1 A
    Q2a1a4a1 L619.2 G->C 1 A
    Q2a1a4a2 BZ3920 A->G 2 A
    Q2a1c FGC4675 A->T 1 A
    Q2a1c1a FGC4891 C->A 1 A
    Q2a1c1a2~ L327^^ T->C 1 A
    Q2a1c1b1b~ BZ3115 G->T 3 A
    Q2a1c2b Y29493 C->G 1 A
    Q2b Y1189 G->A 6 A
    Q2b YP751 G->A 1 A
    Q2b Y1172 C->T 2 A
    Q2b Y1190 G->C 4 A
    Q2b YP750 G->T 3 A
    Q2b1a1b2~ BZ530 G->T 3 A
    Q2b1b~ BZ488 G->A 1 A

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  9. #15
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    Y-haplogroup predictions from cladefinder.

    NE3

     


    NE4 - BY157129 G -> A (1 read), BY55394 C -> T (1 read) (most likely false calls and NE4 along with NE3 and NE5 are C-F3447)

     


    NE5

     


    NE8

     


    NE30

     


    NE39

     


    NE45 - CTS4793 C -> G ( 1 read)

     


    NE56

     


    So far the overwhelming majority of the samples have been C-L1373 and downstream.
    Last edited by altvred; 05-27-2021 at 10:19 PM.

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  11. #16
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    Y-DNA (P)
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    Quote Originally Posted by altvred View Post
    Y-haplogroup predictions from cladefinder.

    NE3

     


    NE4 - BY157129 G -> A (1 read), BY55394 C -> T (1 read) (most likely false calls and NE4 along with NE3 and NE5 are C-F3447)

     


    NE5

     


    NE8

     


    NE39

     


    NE45 - CTS4793 C -> G ( 1 read)

     


    NE56

     


    So far the overwhelming majority of the samples have been C-L1373 and downstream.
    Pretty much expected. This clade was also found in Devil's Gate and UKY001. I guess it was once *the* Y-haplogroup in Northeast Asia.
    Y-DNA: R1b-U152 > L2 > Z367 > Z34 > Z33 > BY164497> BY3604 > FT190670 (Réveillon, Orne, France)

    mtDNA: X2 (probably X2m1) Calabria, Italy

    Maternal Y-DNA: J2a-M67 > Z1847 > Y4036 > Z467 > Z447> L210 (Calabria, Italy)

    Paternal mtDNA: K1b2b (France)

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  13. #17
    I hate that this paper is behind a paywall
    Last edited by Administrator; 05-28-2021 at 04:18 AM. Reason: Copyright infringing content removed.

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  15. #18
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    NE8

     


    That's weird Cladefinder assigned NE8 to C-F1699 because in the journal it was originally assigned to DE:

    NE-8 M AR11K AR13-10K 11,601–11,176CalBP D4o DE
    Last edited by Shuzam87; 05-28-2021 at 01:52 AM.

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  17. #19
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    Quote Originally Posted by Shuzam87 View Post
    NE8

     


    That's weird Cladefinder assigned NE8 to C-F1699 because in the journal it was originally assigned to DE:

    NE-8 M AR11K AR13-10K 11,601–11,176CalBP D4o DE
    Btw, are the Y and mtDNA results in the supplementary tables or do you need to access the full paper to see the results? Anyway, highly doubtful all these calls are wrong and this sample isn't C2 like the rest of them.

     


    Quote Originally Posted by alchemist223 View Post
    Pretty much expected. This clade was also found in Devil's Gate and UKY001. I guess it was once *the* Y-haplogroup in Northeast Asia.
    Agreed, certainly, C-F1699 lost some real estate to N in the north and presumably O in the south but in its modern distribution it's still doing a lot better than its European relative subclade
    Last edited by altvred; 05-28-2021 at 03:39 AM.

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  19. #20
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    The paywall is a bummer, but we might get a peek of the paper some other way. Usually supplementary info is made public and that scratches the itch. Based on what I can make out of the PCA, AR33K indeed clusters near Tianyuan. This is great because it evidences that modern East Asian drift wasn't yet established ~30kya.

    AR19K shows more modern East Asian drift and clusters in a way consistent with a very early Northern East Asian (as suggested in the qpgraph). In fact, the sample's off-center position might suggest it hasn't fully drifted away from Tianyuan yet. It could also not be fully differentiated from Southern East Asians either. The Huang paper estimated that Northern and Southern East Asian branches split off ~23k BP. This sample's apparent intermediate drift might be consistent with that hypothesis. I also wouldn't be surprised if the Amur River Basin people of this period are ancestral to the later Proto-American lineage. AR14K and later samples show fully modern Northern East Asian drift. So by at least 19k BP, you have fully drifted East Asians and by at least 14k BP you have fully drifted Northern East Asians. This is all based on the PCA and qpGraph mind you. Maybe details from the paper will be more enlightening.
    Last edited by Michalis Moriopoulos; 05-28-2021 at 03:58 AM.
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