@Agauger so good to see you here again.
There are several examples of this. One very commonly known one is that transitions are simultaneously:
- More common than transversions. The cause of this is at least in part because of the biochemistry of mutations.
- More likely to be a conservative amino acid substitution. This cause of this at least in part is the structure of the of the genetic code.
Because fitness is intertwined with mutational bias in this case it is hard to untangle some key features of the data. An example of one attempt to do so is here: Ratios of Radical to Conservative Amino Acid Replacement are Affected by Mutational and Compositional Factors and May Not Be Indicative of Positive Darwinian Selection | Molecular Biology and Evolution | Oxford Academic.
There are other examples too.
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Recombination allows for shuffling of a genome in a manner very likely not to cause harm, and increases (perhaps even dramatically) the chance of causing benefit.
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Copy number variation another example of a mutational mechanism that is not likely to cause harm (thought it sometimes can), but increases the chances of causing benefit.
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Mutational clusters localize point mutations together, which dramatically increases the chance of beneficial coordinated mutations in a protein. These were only recently discovered, and there are several classes. For some of them, we’ve established the bimolecular mechanisms, and expect to for the rest.
All these mutational mechanism are biased towards changes that are more likely to increase fitness. This list is not exhaustive. I could easily double it.
All this is widely agreed upon in the field. Though some specific examples are new, the general pattern has known for a long time, and is not unique to EES. Remember, I am not on board with EES, because this is all already part of evolutionary science.