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Thread: New DNA Papers - General Discussion Thread

  1. #11
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    Quote Originally Posted by lgmayka View Post
    As always, there is the issue of calibrating the results. The paper says:
    ---
    Our results are scaled to real times using a mutation rate of 1.25×10-8 per nucleotide per generation, as proposed recently [16] and supported by several direct mutation studies [14-16]. Using a value of 2.5×10-8 as was common previously [44, 45] would halve the times. This would bring the midpoint of the out-of-Africa separation to an uncomfortably recent 30-40kya, but more concerningly it would bring the separation of Native American ancestors (MXL) from East-Asian populations to 5-10kya, inconsistent with the paleontological record [25, 26]. We suggest that the establishment and spread of the Native American populations may provide a good time point for calibrating population genetic demographic models.
    ---
    This is not entirely convincing, since:

    - There is considerable evidence of some continuing gene flow between the Old and New Worlds after the initial Beringian crossing. I am still skeptical of the recently popular claim that "Mongoloid" characteristics arose independently in the Old and New Worlds.

    - Unlike the authors, I am not "uncomfortable" with some gene flow in and out of Africa continuing until 30,000 B.C. and beyond.
    I agree. I think it is almost impossible that EDAR arose independently in two adjacent populations but not elsewhere (India, Africa, Australia, Europe, etc).
    http://www.anthrogenica.com/showthre...ll=1#post40145

  2. #12
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    Quote Originally Posted by parasar View Post
    Posted by Dienekes:


    Schiffels et al
    Inferring human population size and separation history from multiple genome sequences
    http://biorxiv.org/content/early/201...1/005348?rss=1
    i wonder how accurate Interpretome Chr beta test for the above are:

    mine below

    Father's Mtdna .........T2b17
    Grandfather's Mtdna .......T1a1e
    Sons Mtdna .......K1a4o
    Maternal Grandfather paternal......I1d1-P109
    Maternal side Grandfather .......R1b-S8172
    Wife's Ydna .....R1a-Z282

    My Path = ( K-M9+, TL-P326+, T-M184+, L490+, M70+, PF5664+, L131+, L446+, CTS933+, CTS3767+, CTS8862+, Z19945+, Y70078+ )

  3. #13
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    Quote Originally Posted by Jean M View Post
    J Purps et al., A global analysis of Y-chromosomal haplotype diversity for 23 STR loci, Forensic Science International: Genetics, in press.
    http://www.fsigenetics.com/article/S...084-2/abstract (open access)
    Looks like its 2004 all over again
    Paternal: R1b-U152 >> L2 >> FGC10543, Pietro della Rocca, b. 1559, Agira, Sicily, Italy
    Maternal: H4a1-T152C!, Maria Coto, b. ~1864, Galicia, Spain
    Mother's Paternal: J1+ FGC4745/FGC4766+ PF5019+, Gerardo Caprio, b. 1879, Caposele, Avellino, Campania, Italy
    Father's Maternal: T2b-C150T, Francisca Santa Cruz, b.1916, Garganchon, Burgos, Spain
    Paternal Great (x3) Grandfather: R1b-U106 >> L48 >> CTS2509, Filippo Ensabella, b.~1836, Agira, Sicily, Italy

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  5. #14
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    Hopefully some of the genome bloggers manage to obtain the data from these Greek populations so they can be analysed and compared to modern populations in more detail.

    I would be particularly interested to see how the Cappadocian Greeks compare to Turks from the same region, Cypriots and peoples from the Caucasus.

    EDIT: just noticed the discussion thread - this should probably be moved there.
    Last edited by mnd; 06-10-2014 at 05:59 PM.

  6. #15
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    Quote Originally Posted by vettor View Post
    http://dienekes.blogspot.com.au/2014...aplotypes.html

    neanderthals gave us red-hair

    Eupedia person has been telling us this for years
    Interesting, here I was thinking that the red hair mutation was around 10kybp.

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  8. #16
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    Quote Originally Posted by Mehrdad View Post
    Interesting, here I was thinking that the red hair mutation was around 10kybp.
    The paper refers to skin color, not hair color; and in Taiwanese aborigines (and to some extent other East Asians), not Europeans. From the abstract:
    ---
    Frequency of this Neanderthal introgression is low in Europeans (~5%), moderate in continental East Asians (~30%), and high in Taiwanese aborigines (60-70%). Since the putative Neanderthal introgressive haplotypes carry a loss-of-function variant that could alter the function of MC1R and is associated with multiple traits related to skin color, we speculate that the Neanderthal introgression may have played an important role in the local adaptation of Eurasians to sunlight intensity.
    ---

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  10. #17
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    Quote Originally Posted by vettor View Post
    http://dienekes.blogspot.com.au/2014...aplotypes.html

    neanderthals gave us red-hair

    Eupedia person has been telling us this for years
    I think the paper is about a variant responsible for skin colour in Eurasiatic peopple, very specially the east-asiatic people (the old "yellow" race) and not for the red hair.

    "the Val92Met variant, a loss-of-function variant in MC1R that is associated with multiple dermatological traits including skin color and photoaging."

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  12. #18
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    Quote Originally Posted by vettor View Post
    http://dienekes.blogspot.com.au/2014...aplotypes.html

    neanderthals gave us red-hair

    Eupedia person has been telling us this for years
    This has to do with the skin coloring of Eurasians, mostly Eastern. The cause of red hair is a dysfunctional MC1R. Not the same thing. There is no evidence of red hair, even in the Neolithic to this point.

  13. #19
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    Quote Originally Posted by DMXX View Post
    Fresh off the press; came out a few days ago on PubMed.

    Genetic Diversity of a Late Prehispanic Group of the Quebrada de Humahuaca, Northwestern Argentina.
    Mendisco F1, Keyser C, Seldes V, Rivolta C, Mercolli P, Cruz P, Nielsen AE, Crubezy E, Ludes B. Ann Hum Genet. 2014 Jun 24. doi: 10.1111/ahg.12075. [Epub ahead of print]

    [Link]
    From the Mendisco paper:
    From a total of 51 individuals, the mitochondrial haplogroup status of 41 samples was reproducibly retrieved (Table 2). Each of these 41 individuals belongs to one of the Amerindian major founding mitochondrial haplogroups (Tamm et al., 2007;Achilli et al., 2008; Perego et al., 2010). Eighteen individuals were associated with maternal lineage A2, 12 with lineage B2, six individuals belonged to lineage C1b, and finally, five belonged to lineage D1. Reproducible complete HVR-1 sequences were obtained for 33 of the 51 individuals tested. These 33 sequences were classified into 16 different haplotypes, of which 10 were carried by a single individual whereas six were shared by at least two individuals (Table 2).
    2014_Mendisco_Table2.jpeg
    From a total of 51 individuals, the Y-haplogroup status of 22 individuals was reproducibly determined (Table 3). Eighteen out of the 22 male individuals belonged to the most frequent haplogroup within Amerindian populations, Q-M3 (Battaglia et al., 2013). The remaining three individuals were associated with the haplogroup Q-M346 (Q1a2).
    2014_Mendisco_Table3.jpeg

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  15. #20
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    Ancient y-dna from the americas is not exciting because it always turns out to be Q.
    Maternal Uncle y-line= F0R1b1-L21

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