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

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

    https://www.sciencedirect.com/scienc...92867421005754

    Available online 27 May 2021

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

    XiaoweiMao1HucaiZhang23
    ShiyuQiao145YichenLiu14FengqinChang2PingXie2MingZh ang1TianyiWang16MianLi17PengCao1RuoweiYang1FengLiu 1QingyanDai1XiaotianFeng1WanjingPing1ChuzhaoLei8Jo hn W.Olsen19E. AndrewBennett1 Qiaomei Fu 14510

    https://doi.org/10.1016/j.cell.2021.04.040

    Highlights

    • Tianyuan/AR33K ancestry was widespread in northern East Asia before the LGM
    • The earliest northern East Asian appeared in the Amur region at the end of the LGM
    • The AR14K-related population is the closest East Asian source for Ancient Paleo-Siberians
    • EDAR V370A likely increased to high frequency after the LGM

    Summary

    Northern East Asia was inhabited by modern humans as early as 40 thousand years ago (ka), as demonstrated by the Tianyuan individual. Using genome-wide data obtained from 25 individuals dated to 33.6–3.4 ka from the Amur region, we show that Tianyuan-related ancestry was widespread in northern East Asia before the Last Glacial Maximum (LGM). At the close of the LGM stadial, the earliest northern East Asian appeared in the Amur region, and this population is basal to ancient northern East Asians. Human populations in the Amur region have maintained genetic continuity from 14 ka, and these early inhabitants represent the closest East Asian source known for Ancient Paleo-Siberians. We also observed that EDAR V370A was likely to have been elevated to high frequency after the LGM, suggesting the possible timing for its selection. This study provides a deep look into the population dynamics of northern East Asia.
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    Data and code availability

    Original data for the 25 newly sequenced individuals: Aligned reads (BAM format) and genotype calls (Eigenstrat format) of the nuclear DNA have been deposited in the BIG Data Center Genome Sequence Archive (http://bigd.big.ac.cn/gsa-human/; accession number: PRJCA003699); Mitochondrial DNA (fasta format) have been deposited in the Genome Warehouse in the National Genomics Data Center (https://bigd.big.ac.cn/gwh/; accession number: PRJCA003699) (CNCB-NGDC Members and Partners, 2021; Wang et al., 2017).

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    Quote Originally Posted by Shuzam87 View Post
    Data and code availability

    Original data for the 25 newly sequenced individuals: Aligned reads (BAM format) and genotype calls (Eigenstrat format) of the nuclear DNA have been deposited in the BIG Data Center Genome Sequence Archive (http://bigd.big.ac.cn/gsa-human/; accession number: PRJCA003699); Mitochondrial DNA (fasta format) have been deposited in the Genome Warehouse in the National Genomics Data Center (https://bigd.big.ac.cn/gwh/; accession number: PRJCA003699) (CNCB-NGDC Members and Partners, 2021; Wang et al., 2017).
    Dataset and BAM files are here.

    https://bigd.big.ac.cn/gsa-human/browse/HRA000411

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    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 –
    Last edited by Shuzam87; 05-27-2021 at 05:56 PM.

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    Quote Originally Posted by Shuzam87 View Post
    NE56 M AR19K AR19K 19,587–19,175CalBP G2 C2
    NE-8 M AR11K AR13-10K 11,601–11,176CalBP D4o DE
    Are these the oldest C2 and oldest D (assuming the DE is D) samples to date?

    Quote Originally Posted by Shuzam87 View Post
    NE45 M AR9.2K_o AR9.2K_o 9,425–9,029CalBP G1a1a P
    Would be interesting to find out where it fits in the P tree. Could be a Q as well.

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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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    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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    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.
    Ελευθερία ή θάνατος.

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    Quote Originally Posted by Michalis Moriopoulos View Post
    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.
    I agree with this, Northern East Asia seems overdiscussed on Anthrogenica to the general detriment of Southern East Asia.

    Quote Originally Posted by Kristiina View Post
    @ Ebizur

    You are only quoting Han frequencies. Han Chinese are the most recent layer in China. The older distributions may be hidden rather among the different ethnic minorities.
    I don't really pay attention to haplogroups, but some of the regional variation among Han Chinese (at least in terms of Y-DNA and mtDNA) seems to reflect pre-Chinese substrate populations. To get a better sense of what "older distributions" were, we may also need to look at East Eurasian populations outside of modern-day China.
    Last edited by okarinaofsteiner; 05-30-2021 at 08:56 PM.

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