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Thread: DISCUSSION THREAD FOR "Genetic Genealogy and Ancient DNA in the News"

  1. #2211
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    Quote Originally Posted by Ebizur View Post
    This is not the first time that this refinement of the human mtDNA phylogeny has been suggested. It would nicely parallel the connection between (East) Asia and Africa that is apparent in the relationship between Y-DNA haplogroups D and E.
    Interesting, do you have any previous references handy that suggested this?

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    Quote Originally Posted by rozenfeld View Post
    https://www.theatlantic.com/science/...-price/583636/

    Is DNA Left on Envelopes Fair Game for Testing?

    The genealogist’s dream of testing old, spit-laced artifacts is coming true—but raising questions about who controls dead people’s DNA.
    Sarah Zhang, Mar 1, 2019
    Who said they were dead?
    Some of the mystery envelopes are from possible parents from 30 years ago.
    It is these probably living, and their current families, who bring closest focus to the ethical questions.

    By contrast, a fling with a soldier going off to WW1 is likely to be far better accepted by later descendants.

    Friends are dealing with a number of these situations. From normal DNA testing.
    Chronological and generational proximity always adds emotion. And the difficulty of dealing with that.
    I am surprised at how many encounters have gone well, but these people are respectful of the other parties' position, and gentle with their disclosures.
    Maybe that helps a lot.

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    Quote Originally Posted by blackflash16 View Post
    If I'm not mistaken, they have L3h as being basal to a M/L3(xL3h) clade:

    Attachment 29202
    This is what I could find on Internet on L3h:

    "Of particular interest, however, are haplogroups L3h and L3i (Fig. 3), both of which highly informative, albeit pointing in different directions. Although rare, haplogroup L3h is present across Eastern Africa (Kivisild et al. 2004; Poloni et al. 2009; Soares et al. 2012; Tishkoff et al. 2007). It dates to ~55.1 ka (Soares et al. 2014) with the two basal subclades L3h1 and L3h2 dating to ~47 ka (Behar et al. 2012) and L3h2 to ~31 ka (from our HVS-I network). Intriguingly, all of the major identifiable subclades of L3h are found at high diversity in Sudan, as well as across the rest of Eastern Africa."

    Mosaic maternal ancestry in the Great Lakes region of East Africa: https://core.ac.uk/download/pdf/30733095.pdf

    More info can be found in this paper: Complex Genetic History of East African Human Populations.

    Among other:
    The L3h haplotype is observed at high frequency in Nilo-Saharan speaking populations and at low frequency in East African Afroasiatic speaking populations. Outside of East Africa, the L3h haplotype is observd at low frequencies in a few populations that live in the vicinity of Nilo-Saharan speaking populations.
    Last edited by Kristiina; 03-06-2019 at 07:24 PM.

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    Quote Originally Posted by Kristiina View Post
    From Figure 3 it appears that Ust-Ishim is not closest to Tianyuan B, as assumed before, but to R0/HV.
    Well, yeah, as far as I can tell based on an equal amount of evidence: none. I don't see what support there is for any of these random trees in different papers. There aren't any mutations shared between M and L3(xMN), so why is there a node there at all?

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    This is what the authors explain about their phylogenetic analysis, so everybody can judge by themselves how probable their model is:

    "Phylogenetic analysis

    We performed a Median Joining Network to better explore the phylogenetic position of the two ancient sequences. We selected 8 ancient and 536 modern sequences belonging to different sub-branches of the N haplogroup as well as to the haplogroup L3 and M, plus the rCRS and RSRS reference sequences (Table S6). Alignment was performed with the DNA Alignment software and then visually confirmed. Nucleotide position 16519 as well as the poly-C stretches and AC-indels at positions 16180–16193, 303–315, 515–524 and 573–576 were excluded from the phylogenetic analysis62. The Median Joining Network was calculated by Network v.5 (www.fluxus-engineering.com) giving equal weights to all nucleotide sites. The resulting network was drawn without applying pre- or post-processing steps and visualized by means of Network Publisher.

    BEAST v1.8.063 was used to produce a phylogenetic tree from a multi-sequence alignment containing the mtDNA sequence of TK RS H1, as representative of the haplotype found in Takarkori, and 209 published complete genomes of ancient and modern samples with lineage relevance for main haplogroups and sub-haplogroups (Tables S6 and S7). The best substitution model for the dataset, as determined according to Mega 764, was the Generalised time-reversible with a fixed fraction of invariable sites and gamma distributed rates (GTR + G + I). "
    Last edited by Kristiina; 03-07-2019 at 08:49 AM.

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    Hello, please forgive me if this thread is not appropriate to ask the following question.

    Is someone aware of/could someone speculate what the term "AHG" stands for in the bottom right hand side of the following picture screen-shotted from https://brown.hosted.panopto.com/Pan...6-aa02016a1124 ? Asian Hunter Gatherer??

    picanthrogenica.png

    Also, does the "South Eurasian Early Holocene Cline" showed along with "North Eurasian Early Holocene Cline" at around 18:07 min. (the quality of the visuals is not so great though and I can't read what was written in the slide) in the above lecture include Indian hunter gatherers at its eastern extremities or does it stop at Iranian hunter gatherers before the beginnings of transition to farming in West Asia?

    Thank you very much!

    Edit: My brain worked a little bit a tad late (or it might not have done yet after all); could AHG refer to Andamanese Hunter Gatherer or something? This looks promising but don't they create these types of CHG, WHG, etc. terms for aDNA clusters as opposed to modern ones? Or do they have ancient Andamanese samples instead?

    And regarding the South Eurasian Early Holocene Cline, it seems the cline does include India of the early holocene (pre-Mehrgarh) too since the maroon color used to label South Asian Hunter Gatherers is also present in the characterisation of the cline. Which if true makes me wonder what the most western location was in which the lowest but some significant ancestry of the East Eurasian (Onge-related) part of the early holocene Indian hunter gatherers was present. But somehow all this seems false and not presenting any novel scenario - they might be talking about the usual post-Mehrgarh developments only. That number below the name of the cline which is not quite clear but appearing somewhat like 7000 BCE or something seems to point to this (but then 7000 BCE is still quite early for that cline to already have existed according to the familiar model, no?).
    Last edited by anthroin; 03-09-2019 at 03:49 AM.

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    Not DNA, but potentially may influence interpretation of isotopic data:

    https://www.eurekalert.org/pub_relea...-sim030819.php

    Strontium isotope maps are disturbed by agricultural lime

    Many archeological studies based on strontium isotope signatures may have erroneous conclusions; agricultural lime can dramatically alter the isotopic signature of an area, so that it no longer reflects the values in prehistoric times


    http://advances.sciencemag.org/content/5/3/eaav8083

    Agricultural lime disturbs natural strontium isotope variations: Implications for provenance and migration studies

    Erik Thomsen* and Rasmus Andreasen

    Science Advances 13 Mar 2019:
    Vol. 5, no. 3, eaav8083
    DOI: 10.1126/sciadv.aav8083

    Abstract

    The application of 87Sr/86Sr in prehistoric mobility studies requires accurate strontium reference maps. These are often based from present-day surface waters. However, the use of agricultural lime in low to noncalcareous soils can substantially change the 87Sr/86Sr compositions of surface waters. Water unaffected by agriculture in western Denmark has an average 87Sr/86Sr ratio of 0.7124 as compared to an average of 0.7097 in water from nearby farmland. The 87Sr/86Sr ratio obtained from samples over 1.5 km along a stream, which originates in a forest and flows through lime-treated farmland, decreased from 0.7131 to 0.7099. Thus, 87Sr/86Sr-based mobility and provenance studies in regions with low to noncalcareous soils should be reassessed. For example, reinterpreting the iconic Bronze Age women at Egtved and Skrydstrup using values unaffected by agricultural lime indicates that it is most plausible that these individuals originated close to their burial sites and not far abroad as previously suggested.

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    The Iberian HG paper is actually nice. Apparently there is a clear difference between Iberian Magdalenian and non-Iberian Magdalenian. The paper hints that the latter can be found in MN examples:

    However, our models with Goyet Q-2 as ultimate source highlight not only the admixed nature of La Braña 1 and El Mirón, but also that Goyet Q-2-like ancestry in MN individuals outside Iberia hints at Iberia as one possible source, but not the exclusive source, of the Neolithic in Britain. Further sampling from regions in today’s France, the Netherlands, Belgium, Luxembourg, and Germany is needed to answer this question.
    Also, considering the Villabruna stuff in post-LGM Iberia is old and consistent and can be proven to be an admixture, it means that the Villabruna couldn't have originated all that far from Iberia.
    Last edited by epoch; 03-14-2019 at 09:23 PM.

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    Hmmm!?
    Balma Guilanya` (Late Upper Paleolithic)
    13,380 - 10,990 years cal BP
    BAL0051: mt-U5b2a y-I1
    BAL003: mt-U2'3'4'7'8'9' y-C1a1a

    That's the oldest I1 yet, and isn't C1a1 restricted to Japan and neighbors? BAL003 must have been a typo yes? C1a2a would make perfect sense.
    Last edited by Kale; 03-15-2019 at 03:02 AM.
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    Yes, on yfull all C-M8 samples are from Korea, Japan and China and I am not aware of any other ancient C1a1 sample. Nearly all are C1a2. Kostenki is C1b-F1370.

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