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Although many nucleotide changes that can occur in DNA have no effect on the fitness of the cell, if the nucleotide change enhances the growth of that cell even by a small degree, then the mutant form would be able to increase its relative numbers in the population.
Ninety-one A. phagocytophilum functional pseudogenes of the pfam01617 family were analyzed using maximum parsimony, yielding a tree that included eight major clades containing highly similar sister taxa but which were quite divergent from others, represented by many nucleotide changes at deeper nodes and longer branch lengths (Figure 1).
Many nucleotide changes, both synonymous and nonsynonymous, are expected to be unequivocally neutral because they never lead to any form of phenotypic change in the organism.
Six genes (atp6-1, rps19-p, nad6, nad6, cob and cox2 exon 2) had many nucleotide changes in the (lo) durum and the Ae. longissima genomes compared with the T. turgidum genome.
Despite starting with a newly isogenized line, deep-sequencing identified many nucleotide changes in the rye background relative to the parental control and so considerable mapping was required to pinpoint the relevant mutation.
First, the Japanese eel and medaka were diverged from their common ancestor soon after the TGD without undergoing many nucleotide changes between paralogous chromosomes of their ancestor; therefore, the genomes of two species share relatively few nucleotide changes specific to each exact pair of orthologous chromosomes, which leads to vague orthology assignments among the ohnologous chromosomes.
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MMC does not appear to induce many single nucleotide changes, as indicated by the similar number of events compared to spontaneously mutating strains.
The whole genome is constantly evolving and generates many germ-line nucleotide changes known as single-nucleotide polymorphisms (SNPs).
Furthermore, conversions that copy non-coding sequences into coding regions (e.g. as in the human CYP2A13 gene, discussed below) can introduce new functionality more quickly than point mutations, since many nucleotides are changed by a single event.
This is because these genes are unsuitable for molecular dating of microhylid subfamilies (due to high nucleotide substitution rates [ 3]), and the tyr sequences did not allow us to calculate variance-covariance matrices of branch lengths for the designated topology (Tree1a), possibly due to many nodes lacking supporting nucleotide changes.
However, most of these are assigned to the species that have been studied here, and nucleotide changes in many of these genomes should be treated as polymorphisms.
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