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Thread: A Late Pleistocene human genome from Southwest China

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    A Late Pleistocene human genome from Southwest China

    Turns out the Red Deer Cave people were modern humans.

    A Late Pleistocene human genome from Southwest China
    Current Biology, 2022
    Xiaoming Zhang, Xueping Ji, Chunmei Li, Tingyu Yang, Jiahui Huang, Yinhui Zhao, Yun Wu, Shiwu Ma, Yuhong Pang, Yanyi Huang, Yaoxi He, Bing Su
    Available online 14 July 2022
    ISSN 0960-9822,
    https://doi.org/10.1016/j.cub.2022.06.016.
    (https://www.sciencedirect.com/scienc...60982222009289)

    Highlights

    • Genome sequencing of a Late Pleistocene human (MZR, ∼14.0 kya) in Southwest China

    • MZR represents an early diversified modern human lineage in East Asia

    • Genetic stratification in ancient southern populations of East/Southeast Asia

    • MZR deeply links to the East Asian ancestry that contributed to First Americans

    Abstract: Summary
    Southern East Asia is the dispersal center regarding the prehistoric settlement and migrations of modern humans in Asia-Pacific regions. However, the settlement pattern and population structure of paleolithic humans in this region remain elusive, and ancient DNA can provide direct information. Here, we sequenced the genome of a Late Pleistocene hominin (MZR), dated ∼14.0 thousand years ago from Red Deer Cave located in Southwest China, which was previously reported possessing mosaic features of modern and archaic hominins. MZR is the first Late Pleistocene genome from southern East Asia. Our results indicate that MZR is a modern human who represents an early diversified lineage in East Asia. The mtDNA of MZR belongs to an extinct basal lineage of the M9 haplogroup, reflecting a rich matrilineal diversity in southern East Asia during the Late Pleistocene. Combined with the published data, we detected clear genetic stratification in ancient southern populations of East/Southeast Asia and some degree of south-versus-north divergency during the Late Pleistocene, and MZR was identified as a southern East Asian who exhibits genetic continuity to present day populations. Markedly, MZR is linked deeply to the East Asian ancestry that contributed to First Americans.

    Keywords: Southwest China; Late Pleistocene; hominin cranium; ancient genome; diverse lineage; Maludong; Red Deer Cave; First Americans
    EDIT: Here is the PDF
    Last edited by alchemist223; 07-14-2022 at 11:26 PM. Reason: Added pdf link.
    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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    Alright, this is a pleasant suprise! Too bad the whole thing even supp. is paywalled.
    BAM is here, 250MB
    https://ngdc.cncb.ac.cn/gsa-human/browse/HRA002402
    Does that make for good quality genotype? Fingers crossed
    Last edited by Kale; 07-14-2022 at 05:35 PM.
    Collection of 14,000 d-stats: Hidden Content Part 2: Hidden Content Part 3: Hidden Content PM me for d-stats, qpadm, qpgraph, or f3-outgroup nmonte models.

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    Do they have the y chromosome
    Maternal Uncle y-line= F0R1b1-L21

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    Quote Originally Posted by venustas View Post
    Do they have the y chromosome
    No, MZR was identified as a female.
    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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    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 alchemist223 View Post
    No, MZR was identified as a female.
    M9 mtdna in haplogroup in south shina 14kya this is not that big of news

    I was hoping for a y chromosome
    Maternal Uncle y-line= F0R1b1-L21

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    Quote Originally Posted by venustas View Post
    M9 mtdna in haplogroup in south shina 14kya this is not that big of news

    I was hoping for a y chromosome
    It's very nice to have Pleistocene-era East Asian ancient DNA, especially from a more southern part of East Asia. Every ancient sample matters for reconstructing the past.
    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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    I am skeptical of the papers' claim that MZR is clossely related to Native Americans. Although the article says that MZR forms a clade with Native Americans, they later say that Amur-14kya and UKY "exhibit a higher affinity to the Americans compared to MZR"
    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 alchemist223 View Post
    I am skeptical of the papers' claim that MZR is clossely related to Native Americans. Although the article says that MZR forms a clade with Native Americans, they later say that Amur-14kya and UKY "exhibit a higher affinity to the Americans compared to MZR"
    Me too. MRZ did not have high EDAR like Native Americans do

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    Quote Originally Posted by Diictodon View Post
    Me too. MRZ did not have high EDAR like Native Americans do
    Then again nether does huge parts of East Asia(drops off quick in SEA) in general, nor many early Native American samples(USR1, Anzick-1 and one Brazil_LapaDoSanto_9600BP sample and a Brazil_Laranjal_6700BP sample). Its only near fixation in some present day native Americans(Pima, Karitana), Koreans(I think?) and Tungusic people and so that's likely a fairly recent convergent phenomenon. Don't know if the presence(or lack) of the derived EDAR allele tells us much about MZR's affinities to Native Americans.

    https://www.researchgate.net/publica...-kB_Activation

    https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6327247/

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