In principle, however, step 2 could include the selection of the best model of molecular evolution for any given subset.
To distinguish changes in selection from changes in mutation rate we compared the rate of molecular evolution in a given element with the rate in nearby ancestral repeats.
The different patterns of molecular evolution are intriguing given that several of these HPs interact with one another, and all interact with the well-conserved HP1 (Additional file 1: Supplemental Figure S1).
In view of molecular evolution, DNA methylation gives rise to CpG deficiency [4] [6], because methylated CpG sites will easily mutate to TpG sites [7], [8].
According to a central principle of molecular evolution, the likelihood that a given mutation occurs is independent of the mutation's phenotypic consequences.
This is a kind of risk-free molecular evolution: When multiple copies of a given gene are present in a species' genome, chance mutations in some copies can either ruin the proteins they encode or produce innovative versions; either way, the remaining intact copies still produce the original protein.
Therefore, rapid molecular evolution was not localised to a given region or selection hot spot in the genome and different levels of selective constraint appear to be operating on genes that are separated by relatively small distances.
Given the unusual patterns of molecular evolution found in other chelicerate mitochondrial genomes, we sought to determine whether pseudoscorpion mitochondrial genomes shared any of these unusual properties.
This and other conundrums have led many to believe that RNA may itself be the product of early molecular evolution, and that proto-RNAs arose first and eventually gave way to RNA.
Taken together, our findings led us to propose a model which gives a plausible scenario for the molecular evolution of the PDZ/LIM genes and their diverse gene architecture (Fig. 6).
