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As with gonococcal strain MS11, divergence is indicated by the genomotyping results for the strain FA19 pilC gene, maf-associated hypothetical genes, and prophage-associated genes (Table 2).
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Longevity of the transferred genes is indicated by their divergence from the donor through accumulated mutations.
All amino acid changes for Type II divergence are radical, indicating a change in amino acid properties; the single exception is indicated with 'C'C
Estimated divergence times are indicated on the ML topology in Figure 2. A detailed chronogram is provided in the additional file 3. The standard deviations of all estimates fall between 0.5 to 0.7 Million years (My); this error value is implied in all divergence estimates indicated below.
Divergence time estimates are indicated as mean ± S.D. (95% confidence interval).
Monkey King was actively amplified in Brassica after divergence from Arabidopsis, which was indicated by the prompt increase in copy number and by phylogenetic analysis.
Genes with > 2 SD divergence indicated in bold NAH indicates No Annotated Homologue in the other sequence * probably frame shifted components of the same vacA related gene Genes with > 2 SD divergence in each analysis are indicated in bold NAH indicates No Annotated Homologue in the other sequence It cannot be assumed that all genes identified in this manner have been recently acquired.
Length of branch represents divergence and numbers on branches are indicated as percentage of bootstrap values in 1000 sampling replicates.
Divergence times between different clusters were indicated in a scale of millions of years.
Duplicated genes may have different evolutionary fates [ 54], which can be indicated by divergence in their expression patterns.
Duplicate genes may have different evolutionary fates: nonfunctionalization, neofunctionalization, or subfunctionalization [ 76], which may be indicated with divergence in expression patterns.
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