Douglas Futuyma (2005) p. 162Let’s think about the number of mutations that could accumulate in a population over time. A few pages ago we looked at the origin of antibiotic resistance in bacteria in order to prove that mutations occur randomly. Now we’ll consider just how frequency those mutations could arise in bacteria. Then we’ll ask how frequently mutations occur in humans.
Our model bacterium is Esherichia coli the common, and mostly benign, intestinal bacterium. The entire genome was sequenced in 1997 (Blattner et al., 1997) and its size is 4,200,000 base pairs (4.2 × 106 bp). Every time a bacterium divides this amount of DNA has to be replicated; that’s 8,400,000 nucleotides (8.4 × 106).
The most common source of mutation is due to mistakes made during DNA replication when an incorrect nucleotide is incorporated into newly synthesized DNA. The mutation rate due to errors made by the DNA polymerase III replisome is one error for every one hundred million bases (nucleotides) that are incorporated into DNA. This is an error rate of 1/100,000,000, commonly written as 10-8 in exponential notation. Technically, these aren't mutations; they count as DNA damage until the problem with mismatched bases in the double-stranded DNA has been resolved. The DNA repair mechanism fixes 99% of this damage but 1% escapes repair and becomes a mutation. The error rate of repair is 10-2 so the overall error rate during DNA replication is 10-10 nucleotides per replication (10-8 × 10-2) (Tago et al., 2005).
Since the overall mutation rate is lower than the size of the E. coli genome, on average there won’t be any mistakes made when the cell divides into two daughter cells. That is, the DNA will usually be replicated error free.
However, one error will occur for every 10 billion nucleotides (10-10) that are incorporated into DNA. This means one mutation, on average, every 1200 replications (8.4 × 106 × 1200 is about ten billion). This may not seem like much even if the average generation time of E. coli is 24 hours. It would seem to take four months for each mutation. But bacteria divide exponentially so the actual rate of mutation in a growing culture is much faster. Each cell produces two daughter cells so that after two generations there are four cells and after three generations there are eight cells. It takes only eleven generations to get 2048 cells (211 = 2048). At that point you have 2048 cells dividing and the amount of DNA that is replication in the entire population is enough to ensure at least one error every generation.
In the laboratory experiment the bacteria divided every half hour so after only a few hours the culture was accumulating mutations every time the bacteria divided. This is an unrealistic rate of growth in the real world but even if bacteria only divide every 24 hours there are still so many of them that mutations are abundant. For example, in your intestine there are billions and billions of bacteria. This means that every day these bacteria accumulate millions of mutations. That’s why there’s a great danger of developing drug resistance in a very short time.
Calculating the rate of evolution in terms of nucleotide substitutions seems to give a value so high that many of the mutations must be neutral ones.
Motoo Kimura (1968)I based my estimate of mutation rate on what we know about the properties of the replisome and repair enzymes. Independent measures of mutation rates in bacteria are consistent with this estimate. For example, the measured value for E. coli is 5.4 × 10-10 per nucleotide per replication (Drake et al., 1998). Many of these mutations are expected to be neutral. The rate of fixation of neutral mutations is equal to the mutation rate so by measuring the accumulation of neutral mutations in various lineages of bacteria you can estimate the mutation rate provided you know the time of divergence and the generation time. (Ochman et al., 1999) have estimated that the mutation rate in bacteria is close to 10-10 assuming that bacteria divide infrequently.
The mutation rate in eukaryotes should be about the same since the properties of the DNA replication machinery are similar to those in eukaryotes. Measured values of mutation rates in yeast, Caenorhabditis elegans, Drosophila melanogaster, mouse and humans are all close to 10-10 (Drake et al., 1998).
The haploid human genome is about 3 × 109 base pairs in size. Every time this genome is replicated about 0.3 mutations, on average, will be passed on to one of the daughter cells. We are interested in knowing how many mutations are passed on to the fertilized egg (zygote) from its parents. In order to calculate this number we need to know how many DNA replications there are between the time that one parental zygote was formed and the time that the egg or sperm cell that unite to form the progeny zygote are produced.
In the case of females, this number is about 30, which means that each female egg is the product of 30 cell divisions from the time the zygote was formed (Vogel and Rathenberg, 1975). Human females have about 500 eggs. In males, the number of cell divisions leading to mature sperm in a 30 year old male is about 400 (Vogel and Motulsky, 1997). This means that about 9 mutations (0.3 × 30) accumulate in the egg and about 120 mutations (0.3 × 400) accumulate in a sperm cell. Thus, each newly formed human zygote has approximately 129 new spontaneous mutations. This value is somewhat less than the number in most textbooks where it's common to see 300-350 mutations per genome. The updated value reflects a better estimate of the overall rate of mutation during DNA replication and a better estimate of the number of cell divisions during gametogenesis.
With a population of 6 billion individuals on the planet, there will be 120 × 6 × 109 = 7.2 × 1011 new mutations in the population every generation. This means that every single nucleotide in our genome will be mutated in the human population every 20 years or so.
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