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Thread: A Late Pleistocene human genome from Southwest China

  1. #11
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    Thanks for the pdf link to study. I had only read Dr Su's interview since the study was behind paywall. It was surprising that it turned out to be modern human after years of speculation.

    https://www.sci.news/genetics/red-de...ome-11002.html

    "Ancient DNA technique is a really powerful tool,” said Dr. Bing Su, a researcher at the Kunming Institute of Zoology.

    “It tells us quite definitively that the Red Deer Cave people were modern humans instead of an archaic species, such as Neanderthals or Denisovans, despite their unusual morphological features.”

    In the new study, Dr. Su and colleagues successfully extracted and sequenced ancient DNA from the Red Deer Cave skull and compared it to that of people from around the world.

    They found that the fossil belonged to an individual that was linked deeply to the East Asian ancestry of Native Americans.

    Combined with previous research data, this finding led the team to propose that some of the southern East Asia people had traveled north along the coastline of present-day eastern China through Japan and reached Siberia tens of thousands of years ago."

    They then crossed the Bering Strait between the continents of Asia and North America and became the first people to arrive in the New World.

    “Genomic sequencing shows that the hominin belonged to an extinct maternal lineage of a group of modern humans whose surviving decedents are now found in East Asia, the Indo-China peninsula, and Southeast Asia islands,” the authors said.

    “The finding also shows that during the Late Pleistocene, hominins living in southern East Asia had rich genetic and morphologic diversity, the degree of which is greater than that in northern East Asia during the same period.”

    “It suggests that early humans who first arrived in eastern Asia had initially settled in the south before some of them moved to the north."

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  3. #12
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    Looking through the F3 graph Fig4, MZR's relation to various pops...
    ~0.235 to MA1, ~0.24 for Hoabhinian, ~0.24 for Tianyuan/AR33K, ~0.275-0.28 for AR19K & Jomon, ~0.280-0.285 for UKY, ~0.295 for DevilsCave, peaks at ~0.300 in various Southern populations, such as Taiwan_Hanben_IA.
    MZR was identified as a southern East Asian
    That is by no means a 'Southern East-Asian' pattern. I really want to test this sample for myself, this is giving me strange theories

    Also...
    The aDNA data confirm that she possesses diverse genetic components and represents an early diversified population, suggesting the scenario of more diverse AMH lineages than previously thought
    Lol, they must have a lonely thesaurus
    Last edited by Kale; 08-06-2022 at 09:45 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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  5. #13
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    Quote Originally Posted by Sky22 View Post
    Thanks for the pdf link to study. I had only read Dr Su's interview since the study was behind paywall. It was surprising that it turned out to be modern human after years of speculation.

    https://www.sci.news/genetics/red-de...ome-11002.html

    "Ancient DNA technique is a really powerful tool,” said Dr. Bing Su, a researcher at the Kunming Institute of Zoology.

    “It tells us quite definitively that the Red Deer Cave people were modern humans instead of an archaic species, such as Neanderthals or Denisovans, despite their unusual morphological features.”

    In the new study, Dr. Su and colleagues successfully extracted and sequenced ancient DNA from the Red Deer Cave skull and compared it to that of people from around the world.

    They found that the fossil belonged to an individual that was linked deeply to the East Asian ancestry of Native Americans.

    Combined with previous research data, this finding led the team to propose that some of the southern East Asia people had traveled north along the coastline of present-day eastern China through Japan and reached Siberia tens of thousands of years ago."

    They then crossed the Bering Strait between the continents of Asia and North America and became the first people to arrive in the New World.

    “Genomic sequencing shows that the hominin belonged to an extinct maternal lineage of a group of modern humans whose surviving decedents are now found in East Asia, the Indo-China peninsula, and Southeast Asia islands,” the authors said.

    “The finding also shows that during the Late Pleistocene, hominins living in southern East Asia had rich genetic and morphologic diversity, the degree of which is greater than that in northern East Asia during the same period.”

    “It suggests that early humans who first arrived in eastern Asia had initially settled in the south before some of them moved to the north."
    Well, if the people represented by the MZR sample really originated from SE Asia and traveled north, then we should expect it to be the closest to Onge/Hoabinhian on F3 and the furthest away from ancient samples in Northern China and NE Asia, however that's not the case. She was very distant from Hoabinhian, despite the proximity in location.

    It's much more likely that MZR and her Southern East Asian relatives originated from Northern China and then moved down south than the other way around.

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  7. #14
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    Quote Originally Posted by MNOPSC1b View Post
    Well, if the people represented by the MZR sample really originated from SE Asia and traveled north, then we should expect it to be the closest to Onge/Hoabinhian on F3 and the furthest away from ancient samples in Northern China and NE Asia, however that's not the case. She was very distant from Hoabinhian, despite the proximity in location.

    It's much more likely that MZR and her Southern East Asian relatives originated from Northern China and then moved down south than the other way around.
    I dont think they are talking about MZR specifically but earliest migrations and branching.

    Nothing surprising about MZR showing high affinity with southern Chinese, and not Southeast Asians as they have pointed it out graphical abstract on first page. They are talking about Late Pleistocene south-north divergence within ancient EA branch. It is localized divergence within ancient EA.


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    Quote Originally Posted by Kale View Post
    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
    Has anyone published or shared called SNPs yet on this BAM?

  10. #16
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    Quote Originally Posted by Sky22 View Post
    I dont think they are talking about MZR specifically but earliest migrations and branching.

    Nothing surprising about MZR showing high affinity with southern Chinese, and not Southeast Asians as they have pointed it out graphical abstract on first page. They are talking about Late Pleistocene south-north divergence within ancient EA branch. It is localized divergence within ancient EA.

    The northern route is supported both by archaeology (IUP microlith) and by aDNA (please refer to the Vallini et al 2021 paper), whereas there's no evidence whatsoever for the southern route.

    And the new evidence from the MZR paper also supports a northern origin for Southern East Asians, cause Hoabinhians were roughly contemporaneous with MZR yet MZR was quite distant from them and had a much closer relation to northern samples, this in no way supports the southern route. A northern origin is a much more logical explanation.

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  12. #17
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    Quote Originally Posted by Kale View Post
    Looking through the F3 graph Fig4, MZR's relation to various pops...
    ~0.235 to MA1, ~0.24 for Hoabhinian, ~0.24 for Tianyuan/AR33K, ~0.275-0.28 for AR19K & Jomon, ~0.280-0.285 for UKY, ~0.295 for DevilsCave, peaks at ~0.300 in various Southern populations, such as Taiwan_Hanben_IA.

    That is by no means a 'Southern East-Asian' pattern. I really want to test this sample for myself, this is giving me strange theories

    Also...

    Lol, they must have a lonely thesaurus
    Sorry to ask again but could this be a northern population moving south or partly admixed "southern East Asian" with northern affinities? Appears more northern than Longlin or even the Qihe 11500 BP sample (Qihe_N also)

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    Quote Originally Posted by Max_H View Post
    Sorry to ask again but could this be a northern population moving south or partly admixed "southern East Asian" with northern affinities? Appears more northern than Longlin or even the Qihe 11500 BP sample (Qihe_N also)
    2 things that stand out to me...
    1) strong preference for DevilsCave over AR19K
    2) roughly equal relation to AR19K and UKY

    1) Does not happen in Jomon, Thailand_IA, Vietnam_BA, Taiwan_IA, or Neolithic sites nearby on mainland China.
    It's an indicator of 'Northern' East-Asian ancestry such as Mongolia_N, Baikal_EN, Native Americans, etc. It's also present to a lesser degree in most Chinese_N
    2) Is an even more Northern indicator, does not even occur in Chinese_N outside of Inner Mongolia.

    Interestingly, the currently available ancient samples from Nepal e.g. Chokhopani, etc. almost pass point 2, and pass point 1, though not apparently as strong as MZR.
    I wouldn't be surprised if Nepal has a lot of MZR ancestry, plus a 'Southern' Neolithic population.
    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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    Quote Originally Posted by Kale View Post
    2 things that stand out to me...
    1) strong preference for DevilsCave over AR19K
    2) roughly equal relation to AR19K and UKY

    1) Does not happen in Jomon, Thailand_IA, Vietnam_BA, Taiwan_IA, or Neolithic sites nearby on mainland China.
    It's an indicator of 'Northern' East-Asian ancestry such as Mongolia_N, Baikal_EN, Native Americans, etc. It's also present to a lesser degree in most Chinese_N
    2) Is an even more Northern indicator, does not even occur in Chinese_N outside of Inner Mongolia.

    Interestingly, the currently available ancient samples from Nepal e.g. Chokhopani, etc. almost pass point 2, and pass point 1, though not apparently as strong as MZR.
    I wouldn't be surprised if Nepal has a lot of MZR ancestry, plus a 'Southern' Neolithic population.
    Have you been able to download MZR's BAM file?
    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)

  16. #20
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    Quote Originally Posted by Kale View Post
    2 things that stand out to me...
    1) strong preference for DevilsCave over AR19K
    2) roughly equal relation to AR19K and UKY

    1) Does not happen in Jomon, Thailand_IA, Vietnam_BA, Taiwan_IA, or Neolithic sites nearby on mainland China.
    It's an indicator of 'Northern' East-Asian ancestry such as Mongolia_N, Baikal_EN, Native Americans, etc. It's also present to a lesser degree in most Chinese_N
    2) Is an even more Northern indicator, does not even occur in Chinese_N outside of Inner Mongolia.

    Interestingly, the currently available ancient samples from Nepal e.g. Chokhopani, etc. almost pass point 2, and pass point 1, though not apparently as strong as MZR.
    I wouldn't be surprised if Nepal has a lot of MZR ancestry, plus a 'Southern' Neolithic population.
    So you're saying that despite its location in Southern China (Yunnan), MZR has "northern" East Asian ancestry?
    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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