Compare and contrast mutation rate and mutation frequency.

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Mutation rate refers to the frequency of new mutations per generation in an organism or a population. Mutation rates can be determined fairly precisely in experimental organisms with short generation times, such as bacteria or fruit flies. Human mutation rates are more difficult to determine accurately. Mutation rates can be used as a "molecular clock" to determine the time since two species diverged during their evolution.

Mutation rates differ widely from one gene to another within an organism and between organisms. Generally mutation rates in bacteria are about one mutation per one hundred million genes per generation. While this sounds quite low, consider that the Escherichia coli bacteria in our intestines produce more than 20 billion new bacteria every day, each of which has approximately four thousand genes. This works out to about ten million new mutations in the population every day. In mice, the rate is about one mutation per ten thousand genes per generation. While this is much larger than the rate for bacteria, the mouse generation time is also much greater.

The appearance of rare dominant genetic diseases, such as retinoblastoma, have been used to estimate the mutation rate in the human population. Retinoblastoma is a childhood cancer of the eye and was a lethal condition until recently. Hence almost every case represented a new mutation (because individuals with the condition did not survive to reproduce and pass the genetic propensity for the disease along to their offspring), and the mutation rate could thus be readily estimated. Modern methods indicate that the mutation rate is roughly one mutation per 10,000 genes per generation. With at least 30,000 genes, this means that each person harbors about three new mutations, although this estimate may be off by a factor of ten. There are many more mutations in non-coding portions of DNA, but these are fairly difficult to study because they have no effect on the phenotype of the person.

About 90 percent of human mutations arise in the father rather than the mother. This may be related to the difference in the number of cell divisions required to produce a sperm versus an egg; sperm are produced late in a male's development, compared to eggs, which are produced quite early in the development of a female. Older parents pass on more mutations, and these may be either mutations within a gene or chromosomal aberrations, which are deletions or rearrangements of the chromosomes and involve many genes. Human mutation rates are generally quite similar worldwide. The exception is in local populations that have been exposed to radioactivity from nuclear testing or other sources.

Some mutations arise as natural errors in DNA replication (or as a result of unknown chemical reactions); these are known as spontaneous mutations. The rates of such mutations have been determined for many species. E. coli has a spontaneous mutation rate of 1/108 (one error in every 108 nucleotides replicated). Humans have a higher spontaneous mutation rate: between 1/106 and 1/105 (probably as a result of the higher complexity of human replication).

Mutations can also be caused by agents in the environment; these are induced mutations. Induced mutations increase the mutation rate over the spontaneous rate. Looking at a single mutation in an individual, one cannot tell if the mutation was spontaneous or induced. Induced mutations can only be discerned by looking at the mutation rate in a population, and comparing it to the spontaneous mutation rate for the species. If the observed mutation rate is higher, then induced mutations can be assumed. Agents in the environment that cause an increase in the mutation rate are called mutagens.

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