Evolution: Nucleotide Mutation Rates
If nucleotide mutation rates were the same for all organism and all parts of the genome, they would be the basis for a perfect molecular clock to determine relationships for constructing evolutionary trees. But they are neither the same for all organisms nor even for various portions of the genome for the same organism.
For those wishing a more comprehensive view of the variables, they may be found by searching for nucleotide mutation rates in Wikipedia, or elsewhere, on the internet. To the best of my knowledge, my peers have neither found nor embraced the evidence I have presented in other posts on this blog showing the major errors in the current published articles on the relationships of phyla and the importance of the Pogonophora in demonstrating those relationships.
MUTATON RATE VARIABLES
Some variables are known but not considered in several major studies, thus producing major errors in proposed schemes of animal evolution. A variation produced by different generation times is the major factor affecting rates of origin of phyla when extremely low evolutionary rates occur - as noted elsewhere in this blog for pogonophorans and perhaps nematodes. Most variables would have a proportional affect within the variation caused by generation time. Fortunately, the affect of generation time diminishes to near zero as one approaches the species level.
There are many documented studies showing different rates for different groups of species.
1. Viruses with RNA genomes mutate at a much faster rate than organisms with DNA genomes.
2. Mitochondrial DNA has a faster mutation rate than nuclear DNA.
3. Methylated DNA is more resistant to mutation than DNA that is not methylated, as in sperm which have higher mutation rates than eggs. This is perhaps tied in with the fact that sperm genes may be expressed in the individual produced more than is expressed by genes from the egg. Methylated DNA from the egg may also be a reason that dosage affect on gene expression has less impact than one might expect from comparison with instances where three of a particular chromosome are present. The methylation effect is not total; that is shown by Medel's pea experiments where the flower pigment expressed is dosage dependent, and in humans where the sickle cell gene is less debilitating in the heterozygous condition.
4. Mutations are more likely to occur near sites where chromosomal deletion or insertions have occurred than in more distant locations from those mutated sites on the chromosome.
5. Genetic factors may affect rates; perhaps through variations in function of chromosomal damage repair functions. Rates may be subject to natural selection balancing the value of introducing change versus the stability desired in successful genes.
6. Environmental factors such as variation in background radiation and/or the extremes of deep sea pressure may also affect rates.
7. Generation time is the current source of error in relating major groupings of phyla. This error is also a factor in proposals of a time of origin of humans relative to monkeys and great apes. But it is not a factor in most studies of animals sharing the same species, genus, or family. However it may be more of a factor as one compares orders and classes of animals.
A botanist colleague maintains generation time is not a factor in evolution of flowering plants, although I think that has yet to be proven.
Generation time versus age affects?
The question might be of interest in human evolution because older individuals may be more likely to have experienced mutations in germ cells, especially sperm, whereas eggs may be spared much of the generation time effect by all being produced before birth as well as by having methylated DNA.
I have not given much thought to this as a general factor because it does not seem apparent for animals in the deep sea that were critical in providing the clue of the annelid ancestry of chordates. If long generation time corresponds with more mutations per individual, it would seem to cancel out to some extent the generation time effect in evolutionary rates. The extreme difference of generation time of abyssal animals critical in the early origin of phyla makes cancellation of this type of little importance when considering overall evolutionary trees of the major groups of animals.
The rate of mutations may not have as much to do with evolution as does natural selection. Beneficial mutations, although they are much rarer than other mutations, tend to be incorporated in the species gene pool via natural selection or survival and reproduction of the individuals having them. Whereas deleterious mutations tend to be eliminated. In mammalian species much of the genome is thought to be non-coding and in the regions of the chromosome between the genes or coding regions. Mutations in the non-coding regions are thought to be of little consequence as long as they maintain the chromosomal integrity.
Although rates are not necessarily of major impact on the direction of evolution, they are essential to consider in establishing the branching pattern of evolutionary trees, especially as regard major group relationships.
Joseph G. Engemann Emeritus professor of Biological Sciences, Western Michigan University October 1, 2014