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Thread: D1 mtDNA - Jomon and Native American genetic affinity

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    D1 mtDNA - Jomon and Native American genetic affinity

    Ancient DNA recovered from 16 Jomon skeletons excavated from Funadomari site, Hokkaido, Japan was analyzed to elucidate the genealogy of the early settlers of the Japanese archipelago. Both the control and coding regions of their mitochondrial DNA were analyzed in detail, and we could securely assign 14 mtDNAs to relevant haplogroups. Haplogroups D1a, M7a, and N9b were observed in these individuals, and N9b was by far the most predominant. The fact that haplogroups N9b and M7a were observed in Hokkaido Jomons bore out the hypothesis that these haplogroups are the (pre-) Jomon contribution to the modern Japanese mtDNA pool. Moreover, the fact that Hokkaido Jomons shared haplogroup D1 with Native Americans validates the hypothesized genetic affinity of the Jomon people to Native Americans, providing direct evidence for the genetic relationships between these populations. However, probably due to the small sample size or close consanguinity among the members of the site, the frequencies of the haplogroups in Funadomari skeletons were quite different from any modern populations, including Hokkaido Ainu, who have been regarded as the direct descendant of the Hokkaido Jomon people. It appears that the genetic study of ancient populations in northern part of Japan brings important information to the understanding of human migration in northeast Asia and America. Am J Phys Anthropol, 2009. 2008 Wiley-Liss, Inc.
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    I looked at this some time ago and figured that the reported D1a isn't D1, most likely is D4h2. But I can't get access to the article anymore to check.

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    Quote Originally Posted by Megalophias View Post
    I looked at this some time ago and figured that the reported D1a isn't D1, most likely is D4h2. But I can't get access to the article anymore to check.
    I would like to know this further. looking at the D tree, both D1 and D4h2 have T16325C mutation, If they didn't test the full sequence I believe there could really have been a mistake. what a shame.. How could we know?

    http://www.phylotree.org/tree/D.htm

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    Yeah, D4h2 is by far more probable.

    On Ian Logan mtDNA site there is one D4h2: EU828638 (Ulchi) Starikovskaya (http://www.ianlogan.co.uk/sequences_..._sequences.htm)

    Ulchi live in Amur and Ainu in Hokkaido and Sakhalin across the narrow strait

    https://en.wikipedia.org/wiki/Ulchsk...ap_(blank).svg

    Mtdna analyses have detected geneflow between Ainu and Okhotsk: Comparisons of mtDNA haplogroup frequencies between the Okhotsk people and other Asian populations revealed that the genetic structures of the Okhotsk people are very similar to those of populations currently living around lower regions of the Amur River and the Ainu of Hokkaido. The results support our previous study on molecular phylogeny of mtDNA HVR 1 sequences, and strongly suggest that the Okhotsk people originated around the lower regions of the Amur River and became an intermediate of gene flow from the continental Sakhalin people to the Ainu.
    (https://www.researchgate.net/publica...le_to_the_Ainu)

    Ainu Genetics Fig S14.GIF
    Last edited by Kristiina; 01-30-2018 at 06:21 AM.

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    The correction is in Adachi et al. (2011) - Mitochondrial DNA Analysis of Hokkaido Jomon Skeletons: Remnants of Archaic Maternal Lineages at the Southwestern Edge of Former Beringia):

    "In our previous study (Adachi et al., 2009), some of the Hokkaido Jomon mtDNAs were assigned to the haplogroup formerly named as D1a (Starikovskaya et al., 2005) or D10 (Volodko et al., 2008). According to additional coding region analyses, this haplogroup is now renamed as haplogroup D4h2 (Van Oven and Kayser, 2009)."

    It is still not too far from some Native American as the Anzick sequence (and others) belong to D4h3.

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    Quote Originally Posted by Gisele H View Post
    The correction is in Adachi et al. (2011) - Mitochondrial DNA Analysis of Hokkaido Jomon Skeletons: Remnants of Archaic Maternal Lineages at the Southwestern Edge of Former Beringia):

    "In our previous study (Adachi et al., 2009), some of the Hokkaido Jomon mtDNAs were assigned to the haplogroup formerly named as D1a (Starikovskaya et al., 2005) or D10 (Volodko et al., 2008). According to additional coding region analyses, this haplogroup is now renamed as haplogroup D4h2 (Van Oven and Kayser, 2009)."

    It is still not too far from some Native American as the Anzick sequence (and others) belong to D4h3.
    very well pointed Gisele, they are sister clades. http://www.phylotree.org/tree/D.htm

    It's also interesting to point that D1 is descendant of D4, I personally don't understand why it is a subclade of its own and not D4-something. But ok
    Last edited by Kurumim; 02-02-2018 at 03:20 PM.

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    Quote Originally Posted by Kurumim View Post
    ...It's also interesting to point that D1 is descendant of D4, I personally don't understand why it is a subclade of its own and not D4-something. But ok
    There was a reluctance to change the classification (which everyone was familiar with) when complete sequencing revealed that D1 was a branch of D4. Also D1, D2 and D3 had been used in the Americas before the largest Asian D group became D4.

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    Quote Originally Posted by Gisele H View Post
    There was a reluctance to change the classification (which everyone was familiar with) when complete sequencing revealed that D1 was a branch of D4. Also D1, D2 and D3 had been used in the Americas before the largest Asian D group became D4.
    Well it's a bit confusing for newbies, but now that you explained makes a little sense, but changing the name wouldn't be a bad idea It would even illustrate the relationship between East Asians and Native Americans more clearly.

    for example:
    I have matches in HVR1 with D4b2b and D4j16 people from China, and a Korean D (tested only mtplus)

    Still very very far matches, but they are there.
    Last edited by Kurumim; 02-03-2018 at 01:46 AM.

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    for a layman like myself, is anyone claiming that American Indians did not migrate from N.E. Asia? or is all this just trying to classify which "family" so to speak do certain groups belong?

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    Quote Originally Posted by JerryS. View Post
    for a layman like myself, is anyone claiming that American Indians did not migrate from N.E. Asia? or is all this just trying to classify which "family" so to speak do certain groups belong?
    the second, trying to link the old world with the "new world"
    Last edited by Kurumim; 02-03-2018 at 02:11 AM. Reason: never mind

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