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21 May 2014

Evolutionary Rates - Kimura

Preamble

In his paper, "Evolutionary rate at the molecular level", Kimura (1968) discusses the rate of evolution as found in comparing various contemporary, at the time, studies with respect to nucleotide substitutions. Kimura began with the assumption that most mutations are neutral or nearly neutral, whereas the thinking at time was that most mutations were usually either harmful or helpful. It was Kimura's work that led to Neutral Theory becoming the Null Hypothesis in modern Molecular Evolution.

Kimura, according to my H-Index Calculator, has been cited over 39169 times, has an h-index >10 and a g-index >10.

Methodology

Kimura begins by looking at the paper by Zuckerkandl and Pauling (1965) who compared studies of hemoglobin molecules who found, among mammals, in a chain of about 140 amino-acids there was a change in one amino-acid in a 107 year period. Then Kimura compares Buettner-Janusch and Hill's (1965) study on primate hemoglobin who found a substitution rate of 45x106 years. The study by Kaplan (1965) between were also compared and found a rate of 2.7x106 years.

Here, Kimura makes the assumption that nuclear DNA is similar among most mammals and that the GC content in mammalian DNA is uniform withing a value of 40-44%. Then Kimura assumes that 4x109 of nucleotide pairs are haploid chromosome complements. From this Kimura estimates a substitution rate within the population of ~2 years.

Compared to the 300 generations rate predicted by Haldane's paper (1957), this is a huge contrast. Kimura concluded, Haldane's erroneous fitness factor aside, that this could be accounted for if most mutations were in fact neutral or at least nearly neutral.

Thus the very high rate of nucleotide substitution which I have calculated can only be reconciled with the limit set by the substitutional load by assuming that most mutations produced by nucleotide replacement are almost neutral in natural selection. (Kimura, 1968, p. 625)

The next paper Kimura looks at is the work by Lewontin and Hubby (1966) who studied genetic variation in the fruit fly species Drosophila psseudoobscura and estimated in each individual that 12% of each loci are heterozygous. Kimura assumes that the heterozygosity would be much higher in nucleotide sequences. Since it is evident that the mutation rate in Drosophila is ten times that of humans, Kimura calculates a mutation rate of 1.5x10-5 and checks his calculation by looking at Drosophila neutral mutations, neucleotide pair mutation per generation the fact that the Drosophila genome is 1/20 the size of the human genome to get the same result.

Finally, Kimura looks at Kimura and Crow (1964) who found that for neutural mutations the probability that an individual in a population is heterozygous and if the individual is homozygous differ.

Looking at Watson's work (1965) Kimura finds that in gamete production substitution in base pairs could be 200-2000 and is reduced to ~2 by natural selection.

Conclusions

Firstly, as in my last post, it must be said that Kimura was in no way finding fault in evolution. In fact, Kimura was proposing a new idea to explain why organisms appear to change so quickly with low cost when calculations such as the one by Haldane say it would take a long time and be costly. In fact, Kimura has been proven correct with Neutral Theory being the Null Hypothesis, with Nearly Neutral Theory taking up much of the slack.

Secondly, Kimura has shown that evolution occurs at a even a faster rate than had previously been supposed. Once again, this supports not defeats evolution. This paper in no way shows that genomes are decaying.

Kimura sums up by stating that each generation is producing neutral or nearly neutral mutations that have been largely ignored and are occurring at a very high rate making random drift an important factor of evolution.

Questions to My Opponent

  • Did you actually read the paper before posting it?
  • If yes to the previous question; did you think neutral or nearly neutral mutations indicated that genomes are decaying?
  • Do you think "random drift" indicated genomic decay?
  • What on earth made you think that this paper demonstrated that the evolution of one species to another is impossible when it is a keystone to the modern understanding of evolution?

Bibliography