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Differently from Omar and Ghosh's work, our work only considers first order mutations.
In our case, the step size σ cannot be a single value because each one of the membership functions encoded in the second part of the chromosome is defined over different universes and so requires different order mutations.
The relatively large number of gene order mutations that have occurred in the Campanulaceae chloroplast genomes causes difficulties when interpreting their phylogenetic significance.
Even in cases such as this, with high levels of gene order complexity, cpDNA gene order mutations make excellent phylogenetic markers.
Due to this unprecedented number of gene order mutations, it is not possible to unambiguously determine the evolutionary order of most events or in some cases to even define the events themselves.
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Our inclusion of transposition as a possible mechanism for gene order mutation in the Campanulaceae chloroplast genomes is problematic.
The mitochondrial genomes of flowering plants vary greatly in size, gene content, gene order, mutation rate and level of RNA editing.
First, the abundance of rearrangement events within the family suggests some mechanism that facilitates gene order mutation; transposition is one such process.
Given the above-mentioned numbers of polymorphic ORFs with unknown functions, the importance of the roles of the three evolutionary factors in genome formation may be arranged in the following order: mutation > segment indel > genome rearrangement.
In contrast, for the 10 papers using laboratory alleles the analysis reveals significant negative epistasis (one-sample t-test: t = 2.36, df = 9, P < 0.05), and therefore laboratory evolved second-order resistance mutations have significantly higher costs than predicted from the effects of the first-order mutations.
Second, the current scoring system which assigns mutation scores in the order: missense mutation < inframe indel < mutation in splice sites < frameshift indel = nonsense mutation may be biased toward identifying tumor suppressor genes over oncogenes.
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