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Given their small size and high rate of evolution, several considerations should be kept in mind when applying comparative molecular forensic analyses to viruses.
Although many mutations in mitochondrial tRNA genes and coding regions have been shown to cause diseases, the high rate of evolution of mtDNA creates many new polymorphic sites.
We sequenced the ND2 (NADH dehydrogenase subunit two) gene and flanking tRNA genes, a region particularly useful for intraspecific and intrageneric studies because of its relatively high rate of evolution [52], [53].
We hypothesize that the limit to deletion sizes will have been reached, given the high rate of evolution typical for viruses and the time window of almost a decade.
In common with other studies generating and analyzing whole mtDNA sequences for interspecific comparisons (e.g. [23]) we noted that the control region tends to contain sites with missing data and because of its high rate of evolution can be difficult to align among species.
However, we did not observe such burst of high rate of evolution in Brassicaceae psbA.
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"In these cases, we find high rates of evolution, meaning when we compare sister species, they tend to be very different from one another," Dr. Thomas said.
Due to the high rates of evolution of ITS sequences, strong support for deep nodes – such as those observed in the multilocus datasets – were not expected in the ITS trees.
Genes that encode products with exogenous targets, which comprise an organism's "exogenome," typically exhibit high rates of evolution.
Genes acting at the extracellular compartment have been reported to exhibit high rates of evolution [ 20, 47].
Previous studies (e.g.,[ 27]) showed long-branch attraction artifacts in phylogenetic reconstruction of the anuran tree due to high rates of evolution of mt DNA in neobatrachians.
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