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Guide to Patagonia's Monsters & Mysterious beings

I have written a book on this intriguing subject which has just been published.
In this blog I will post excerpts and other interesting texts on this fascinating subject.

Austin Whittall


Monday, October 26, 2015

The age of the mtDNA from Upward Sun River in Alaska


The paper by Justin C. Tackney et al., (2015) Two contemporaneous mitogenomes from terminal Pleistocene burials in eastern Beringia, PNAS doi: 10.1073/pnas.1511903112, published today has found that the remains of a stillborn baby and a very young infant that were buried at the same time in a grave in Upward Sun River, Alaska 11,500 years ago, belong to Mitochondrial DNA types C1b and B2, and these "allowing us to refine younger coalescence age estimates for these two clades. C1b and B2 are rare to absent in modern populations of northern North America. Documentation of these lineages at this location in the Late Pleistocene provides evidence for the extent of mitochondrial diversity in early Beringian populations, which supports the expectations of the Beringian Standstill Model.".


Though it is behind a paywall, the information published online indicates the ages of "about 12,800 years ago for C1b and 12,000 years ago for B2" and that one of the paper's co-authors "O'Rourke suspects the real times were even earlier, but that nonetheless both 11,500-year-old infants were at or near the root of their respective genealogical trees".


Additionally, O'Rourke said "'You don't see any of these lineages that are distinctly Native American in Asia, even Siberia, so there had to be a period of isolation for these distinctive Native American lineages to have evolved away from their Asian ancestors. We believe that was in Beringia,'".


This value of 12 to 12.8 kya is interesting. Why not 20 or 25 kya? It is convenient that the these 12,000 years situate the origin of these haplotypes at the time of a purported Beringian standstill. Lets see how they were calculated.


The Supplemental information, on page 4 tells us that "... Mutational distances were converted into years using a corrected molecular clock proposed by ref. 27 or a whole-genome substitution rate of 2.67 × 10−8 sub per site per year".


And this is a critical point, because based on this mutation rate is that the authors have estimated the age of these mtDNA haplotypes.


However this mutation rate is questinable. For instance a value of 0.43 × 10−9 per site per year was reported for the 45,000 year old shin bone from Ust’-Ishim.


The difference between 0.43 x 10-9 and 2.67 x 10-8 (which I will express as 26.7 x 10-9) is 62 times!


I eliminated the previous paragraphs because I was using autosomal and mtDNA mutation rates and they are not comparable. (see the comment below dated 27/Oct.) However, the following is valid. Because as I mention in Comments below, the mtDNA mutation rates estimated by different authors vary and considerably, from 1.3 to 3.2 x 10-8. Even the range for a 95% Confidence Interval is too wide for my liking, so...


Fidgeting with mutation rates one can get a wide range of coalescence dates...and that means you can get mistaken ones too.


I posted in June 2014 about mtDNA C1 haplogroup and in that post, I cited a paper that gave the following age to C1b: 17.9 +⁄- 2.3kya. Which is at odds with the figure calculated by Tackney's team.


In that post, besides questioning the molecular clock (I always seem to be irked by this subject), I wrote: "Interesingly, C1 has a high values for nucleotide diversity indices, and show a South to North cline (with most variations in South America), indicating that it has deeper roots in the southern part of the New World or that bottlenecks reduced its diversity in the North. In my opinion in points at an older date of entry into America than those mentioned above.", which again seems to be at odds with such early (12 kya) dates and a late Beringian standstill.



 C1 mtDNA hg map
A Map showing the mtDNA C1 haplogroup current and probable archaic range
Copyright © 2015 by Austin Whittall

Let's wait and see if they can get a Y chromosome haplogroup from the remains (but it seems both were girls).



Patagonian Monsters - Cryptozoology, Myths & legends in Patagonia Copyright 2009-2015 by Austin Whittall © 

4 comments:

  1. I am not a true believer in the mitochondrial clock, but the quote you link to refers to the *autosomal* mutation rate. From the Ust'-Ishim man paper:
    "We also calculated an independent estimate of the mtDNA mutation rate using the carbon date obtained for the Ust’-Ishim femur together with the mtDNAs of 311 present-day humans. When repeating the above model comparisons and MCMC with BEAST, we obtain a mutation rate of 2.53 ×10^-8 substitutions per site per year (95% HPD: 1.76-3.23 × 10^-8) for the complete mtDNA."

    Directly converting the above estimates to the Ust'-Ishim rate would give a range of around 10-19 thousand years ago for B2 and C1b.

    ReplyDelete
    Replies
    1. Thank you for your comment. That was a serious mistake I made! Autosomal and mtDNA are very different so it is correct to have different rates of differnt orders of magnitude.
      So that point is wrong and I will eliminate it from the post.

      But look at the confidence interval 1.76 to 3.23... rather wide.
      Which is also in line with this paper http://www.biomedcentral.com/content/pdf/s13323-015-0022-2.pdf has a table with a comparison of different mutation rates proposed for mtDNA that range from 1.3 to 2.67 x 10-8.
      Also rather "ample" range.
      thanks again

      Delete
  2. Regarding mutations in general and the "molecular clock", please read this:

    "Even if the overall European mutation rate increase was small,
    it adds to a growing body of evidence that molecular clock
    assumptions break down on a faster timescale than generally
    assumed during population genetic analysis. It was once assumed
    that the human lineage’s mutation rate had changed little since
    we shared a common ancestor with chimpanzees, but this assumption
    is losing credibility owing to the conflict between direct
    mutation rate estimates and molecular-clock-based estimates (8,
    9). Although this conflict might have arisen from a gradual decrease
    in the rate of germ-line mitoses per year as our ancestors
    evolved longer generation times (12, 13), the results of this paper
    indicate that another force may have come into play: change in
    the mutation rate per mitosis. If the mutagenic spectrum was
    able to change during the last 60,000 y of human history, it might
    have changed numerous times during great ape evolution and
    beforehand."
    From http://www.pnas.org/content/112/11/3439.full.pdf
    Evidence for recent, population-specific evolution of
    the human mutation rate, Kelley Harris . Vol. 112 no. 11, 3439–3444, doi: 10.1073/pnas.1418652112 March 17, 2015

    ReplyDelete
  3. Thanks, very interesting paper I had not seen before.

    ReplyDelete

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