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  • Neanderthal/Human divergence

    I have some interest in the field of anthropology and evolution but my knowledge in these fields is rather limited. Just recently I got involved in the discussion about the origins of modern humans and Neanderthals. I have read some seminal papers in the field as Krings et al., 1997, Krings et al., 1999, Ovchinnikov et al., 2000 to get some arguments but I had some difficulties in data interpretation in these articles.

    My opponent says that if human and neanderthal sequences differ in around 35 positions and human (and diverge at 500 000 ya) and chimpanzee in around 60 postions (Krings, 1997 gave 55, Krings 1999, gave 93) then if we take the substitution rate the same for these comparisons (because human/chimpanzee divergence served as calibration point) the time for human/chimpanzee divergence will be in the range of 1,5 million years, which is senseless. I know that something is wrong in this logic, because Krings, 1999 gave the neanderthal/chimp difference as 94 bp. But I cannot reproduce simple and understandable way of calculation of species divergence age. I think that not all information was presented in papers because it is regarded as a basics for evolutionary biology. I have rather poor background in the field of evolution rates quantitation.

    Can you, please, help me to produce the understandable and simple interpretation of the data in the papers, i.e. how to convert the differences in the sequences to the evolutionary divergence age for human/human/, neanderthal/human, human/chimp, neanderthal/chimp? I tried myself the simple quantification based on Krings, 1999 (substitution rate - 0.94x10-7 per site per year per lineage) paper but I got quite strange results that do not correlate to the paper, so I presume that I did not understand methodology:


    Humans/chimps = 2,9 mln ya

    Neanderthals/chimps = 2,94 mln ya

    Hum/Hum = 344 000 ya

    Hum/Neand = 1 mln ya

    I will be very grateful for any hints or help because this situation drives me crazy.

  • #2
    Human and Neanderthal divergence calculations

    Hi AAM,

    I can't answer your question at the moment, but I shall see if I can find out for you.
    Hopefully I can give you an answer soon (otherwise, it might take me a few days).

    Just one thought I've had in the meantime is that the papers that show different differences between chimps & humans might be looking at different areas of DNA or, one paper might be looking at a smaller stretch of DNA (& thus will have a smaller number of sequence differences because the number of sequences being compared is smaller).

    Angela.
    AngelaC
    Registered User
    Last edited by AngelaC; 9 December 2004, 07:20 AM.

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    • #3
      Hi, Angela!

      > I can't answer your question at the moment, but I shall see if I can find out for you.

      Thank you!

      >Just one thought I've had in the meantime is that the papers that show different differences between chimps & humans might be looking at different areas of DNA or, one paper might be looking at a smaller stretch of DNA (& thus will have a smaller number of sequence differences because the number of sequences being compared is smaller).

      Yes, I know it and my opponent knows. Th problem is how to convert the base pair difference in time of divergence. I made quantification on the second paper (Krings,1999) and the results do not correlate with that reported. The quantification on data from the first paper Krings (1997) looks the same crazy in my hands despite diffrent substitution rate and the length of compared fragment.

      In Krings (1999) difference between chimps and humans 93 bp for 5 mln.years (calibration point). If we take the same rate and will estimate the neanderthal/human divergence then we will get 1,9 mln. years, and this is wrong. I have missed something in methodology.

      Articles I mentioned:

      Krings, 1999:
      http://www.ncbi.nlm.nih.gov/entrez/q..._uids=10318927

      Krings, 1997:
      http://www.ncbi.nlm.nih.gov/entrez/q...t_uids=9230299

      Ovchinnikov, 2000:
      http://www.ncbi.nlm.nih.gov/entrez/q..._uids=10761915

      Comment


      • #4
        "Wonky results" from formulas

        Originally posted by AAM
        Humans/chimps = 2,9 mln ya

        Neanderthals/chimps = 2,94 mln ya

        Hum/Hum = 344 000 ya

        Hum/Neand = 1 mln ya

        I will be very grateful for any hints or help because this situation drives me crazy.
        Hi AAM,

        I've been looking at a few papers, especially Krings 1999, during the day, - and you are correct, calculations made from the numbers in Krings 1999 do look "rather wonky".

        I should mention here that my scientific training never involved quantification of lineage divergence times from molecular data ( so my help here is pretty much along the lines of the blind leading the blind).

        For the benefit of everyone else following this thread I'll write down the figures the paper gives for the basepair differences between the sets of comparisons, and the divergence time estimates given in the paper.
        Average difference , Time estimate
        Human-Human 10.9 base pairs , 163, 000 years
        Human-Neanderthal 35 base pairs , 465,000 years
        Human-Chimp 94.1 base pairs , 4-5 million years

        I haven't yet come to any firm conclusions, but my current idea is that we are getting bizarre results from the figures because we are (or at least I was) treating the following sentance as if it were a formula:
        The resulting genetic distances and the estimated age of the modern human–chimpanzee split of 4–5 million years were used to calculate the substitution rate of 0.94 x 10-7 substitutions per site per year per lineage
        When,...it really isn't. What we might be missing is what three "per"s do to the calculation.

        Have you looked at the paper they quote as containing the dating method?
        If not, here is a link to a .pdf of the paper:
        Tamura 1993
        Tomorrow I will see if I can understand the paper (there are lots of scary looking mathematical formulas in it)
        One thing I keep wondering is precisely what they mean by "per lineage" (species?, or each mitochondrial DNA sample?)...that might be whats making the difference between the calculations we are making, and the proper one.

        Angela.

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        • #5
          Hi, Angela!

          Any success in estimation? Or it is too much complicated?

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          • #6
            Originally posted by AAM
            Hi, Angela!

            Any success in estimation? Or it is too much complicated?
            Hi AAM,

            I'm completely baffled!,
            The only thing I can figure out is that the calculations may be derived not from the average difference between each species being compared, but could be caculated by taking the difference from each of the sample pairs (eg. difference between chimp 1 human 1, chimp 1 human 2 etc. going through all the permutations of sample combinations .....at least I think that's what they were saying in Tamura (1993)

            Angela.

            Comment


            • #7
              Originally posted by AngelaCP
              Hi AAM,

              I can't answer your question at the moment, but I shall see if I can find out for you.
              Hopefully I can give you an answer soon (otherwise, it might take me a few days).

              Just one thought I've had in the meantime is that the papers that show different differences between chimps & humans might be looking at different areas of DNA or, one paper might be looking at a smaller stretch of DNA (& thus will have a smaller number of sequence differences because the number of sequences being compared is smaller).

              Angela.
              angela in the show i saw about neadethals beling like us they said the ridge in the skull was from the way they ran.

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              • #8
                Neandertal Gene Study Reveals Early Split With Humans:
                http://news.nationalgeographic.com/n...nderthals.html

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