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Thread: New DNA Papers - General Discussion Thread

  1. #2211
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    Quote Originally Posted by pmokeefe View Post
    Using both newly generated and publicly available data, we examined 280 SNPs flanking the 370A SNP in 51 worldwide populations in order to assess the origin of 370A. Haplotype analysis supports a single origin of the derived allele (Figure 1A), with the mutation lying on a unique, nearly unbroken haplotype extending more than 100 kb among both East Asians and Native Americans.[/INDENT]
    That's pretty interesting, should be easy to test whether it was a Denisovan introgression then, yes?
    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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  3. #2212
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    Quote Originally Posted by Webb View Post
    Reminds me of Professor Wolpoff's Regional Continuity Theory.
    These authors had a paper out in 2017 that was similar, if not even more against African origins.
    It is notable that other researchers from the same country do NOT share this stream of thought.

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  5. #2213
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    Quote Originally Posted by Saetro View Post
    These authors had a paper out in 2017 that was similar, if not even more against African origins.
    It is notable that other researchers from the same country do NOT share this stream of thought.
    The strong form of multiregionalism as either a partisan camp or a vein of thought has been more common in China than elsewhere. I'm not saying that it is a view held by most Chinese scientists in the DNA era. I'm only saying that there is a precedence of rejecting OOA in China.

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    Quote Originally Posted by Saetro View Post
    These authors had a paper out in 2017 that was similar, if not even more against African origins.
    It is notable that other researchers from the same country do NOT share this stream of thought.
    Wolpoff, for me, stands out because he was featured in many Discovery Channel specials where differing theories of the development of modern man were represented. This was before the advent of DNA. It just never made much sense to me that modern man suddenly developed from archaic hominids, simultaneously, in different continents. Now, I do think we can theorize that there were a few different genetic "Edens", so to speak where our ancestors enjoyed major expansions. The relationship of Ydna O,P, R, and Q come to mind in a location close to Siberia/Asia/ Eurasian Steppes. But, I don't think they just showed up on their own. They obviously traveled there from somewhere else.

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  9. #2215
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    Quote Originally Posted by rozenfeld View Post
    https://www.genetics.org/content/ear...ics.119.302368

    A Rare Deep-Rooting D0 African Y-Chromosomal Haplogroup and Its Implications for the Expansion of Modern Humans out of Africa

    Marc Haber, Abigail L. Jones, Bruce A. Connell, Asan, Elena Arciero, Huanming Yang, Mark G. Thomas, Yali Xue and Chris Tyler-Smith

    Genetics Early online June 13, 2019; https://doi.org/10.1534/genetics.119.302368

    Abstract

    Present-day humans outside Africa descend mainly from a single expansion out ∼50,000-70,000 years ago, but many details of this expansion remain unclear, including the history of the male-specific Y chromosome at this time. Here, we re-investigate a rare deep-rooting African Y-chromosomal lineage by sequencing the whole genomes of three Nigerian men described in 2003 as carrying haplogroup DE* Y-chromosomes, and analyzing them in the context of a calibrated worldwide Y-chromosomal phylogeny. We confirm that these three chromosomes do represent a deep-rooting DE lineage, branching close to the DE bifurcation, but place them on the D branch as an outgroup to all other known D chromosomes, and designate the new lineage D0. We consider three models for the expansion of Y lineages out of Africa ∼50,000-100,000 years ago, incorporating migration back to Africa where necessary to explain present-day Y-lineage distributions. Considering both the Y-chromosomal phylogenetic structure incorporating the D0 lineage, and published evidence for modern humans outside Africa, the most favored model involves an origin of the DE lineage within Africa with D0 and E remaining there, and migration out of the three lineages (C, D and FT) that now form the vast majority of non-African Y chromosomes. The exit took place 50,300-81,000 years ago (latest date for FT lineage expansion outside Africa - earliest date for the D/D0 lineage split inside Africa), and most likely 50,300-59,400 years ago (considering Neanderthal admixture). This work resolves a long-running debate about Y-chromosomal out-of-Africa/back-to-Africa migrations, and provides insights into the out-of-Africa expansion more generally.
    Good they revisited the Nigerian DE*
    Very interesting to find such a deep split of the D line in Africa. I was expecting the DE to turn out on the E line. I would not say that this resolves the long running debate since it is from modern DNA, but it surely supports OoA.

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  11. #2216
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    Now geneticists should revisit also the Tibetan DE samples mentioned in this new paper:

    According to this interpretation, the reported Tibetan DE* chromosomes (Shi et al. 2008) would most likely represent back-mutations or genotyping errors at the one SNP used to define haplogroup D, but require further investigation.

    The result of this Haber et al paper would have been more conclusive if they had resolved the position of the Tibetan DE* chromosomes in the DE tree.

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    New split time estimates from this paper are pretty interesting. Haplogroup CT split keeps getting pushed back...now estimated at 101kya.

    CT's split would more or less represent the latest that Basal Eurasian could have split from Basal African lineages, no?

    Last edited by K33; 06-14-2019 at 09:46 PM.

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    Quote Originally Posted by K33 View Post
    New split time estimates from this paper are pretty interesting. Haplogroup CT split keeps getting pushed back...now estimated at 101kya.

    CT's split would more or less represent the latest that Basal Eurasian could have split from Basal African lineages, no?

    That is, if that split was also the split between Basal Eurasian and Basal SSA. The paper however seems to suggest that there was one OoA migration and calibrates that to roughly 50,000-60,000 year ago, based on Neanderthal admixture. It doesn't mention Basal Eurasian at all, which I think is a pity.

    A split dated to 101 kya does coincide with the Skhul and Qafzeh finds.

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  17. #2219
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    Quote Originally Posted by vettor View Post
    https://www.academia.edu/39222183/Ha...ine_Bronze_Age

    Haplogroup J-Z640-Genetic Insight into the Levantine Bronze Age

    This article aims at researching the evolution of J-Z640 using an interdisciplinary approach in order to clarify the leading historical and anthropological events that shaped this particular branch of the human Y chromosome. We compiled a STR (short tandem repeat) and SNP (single nucleotide polymorphism) dataset of 145 known or predicted J-Z640 samples among the customers of Family Tree DNA and Full Genomes Corporation, as well as publicly available samples. Amongst these, we analyzed the results of 41 samples that had undergone Next-Generation Sequencing (NGS) and 32 samples that had undergone SNP testing using Sanger Sequencing. From this data, we constructed a J-Z640 phylogenetic tree that was dated using the method. Our data revealed that Haplogroup J-Z640 is a Y chromosome lineage found most notably, in several minority groups within the Near East such as the Samaritans, Druze, Armenians and Jews. J-Z640 originated during the Bronze Age, most likely in the Levant. During the Bronze Age the haplogroup rapidly expanded with multiple ancient branches surviving to the present, evidencing population growth. Further population expansion, and contraction, was also observed in later periods. Based on its geographic dispersal and age of the haplogroup and its subclades, the founder population most likely belonged to Canaanites found in the Levant. Following the collapse of the late Bronze age system, from the Iron Age onwards there followed a period of “differentiation by culture”, with many of the ancient branches surviving to the present separated along ethno-religious lines.
    I find difficult to put in accordance to their abstract by considering the Yfull tree of J-Z640 :
    https://www.yfull.com/tree/J-Z640/

    Only some sub-branches could enter into the conclusions of the abstract .
    Last edited by palamede; 06-24-2019 at 10:39 AM.

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    Regarding this new paper:

    Some interesting results in there, including what I believe is the first attempt to break down the European ancestry of "Euro Americans" into clusters -- see the bar chart on p. 27 of the paper.

    For those of us with mild colorblindness having trouble with the 5 different shades of blue they use (!), there's a numerical breakdown of these European-American ADMIX clusters on p. 12 of the Supp Data pdf:

    France: 37%
    Great Britain: 25%
    GreeceSouthItaly: 14%
    CentralEurope1/2: (seems basically like Germany + Austria-Hungary + Polish-Lithuanian Commonwealth): 13%
    Scandinavia: 6%
    North Italy : 4%
    Spain/Portugal: 2%
    ---------------------------

    Of course, genuine "French" ancestry is pretty rare in the US, restricted mainly to descendants of early Huguenot settlers in the south, and Catholics in New Orleans and to a lesser extent New England. Therefore it seems the "French" component is capturing a lot of Americans with self-declared German ancestry, especially since many German-Americans seem to have roots in "Frankish" (ie, West) Germany.

    France from north to south also forms a centroid between "Northern Europe" and "Southern Europe", if you opt for a latitudinal division of Europe. So depending on how fine-scaled their admixture analysis goes, probably a lot of American "mutts" -- especially quite common mixtures involving say, Italians and Irish -- wind up leaving a "French" autosomal signal after recombination.

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