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We then used genome sequenced strains to determine the PPC cutoff values depending on the level of divergence of a test strain from the reference strain.
Hence, the level of divergence of the core genome within A. baumannii is strikingly lower than between A. baumannii and its closest species, 13TU (4.6% on average).
The low level of divergence of COI at Easter Island could also be explained by a recent selective sweep of the mitochondrial genome, but the high haplotypic diversity at COI suggests this is not the case.
If the high level of divergence of the sequences is due only to a relaxation of the selective constraints on the encoded proteins, incorporating dN/dS>1 does not provide a significant higher likelihood than models where all codons are forced to have dN/dS≤1.
Based on the level of divergence of EHEC 2 LEE genes from O157 LEE genes, strains clustered into two major groups.
This is problematic because the probabilities of each misclassification will rarely equal each other and are conditional on the level of divergence of the two sequences in question.
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The levels of divergence of MDL1 and MDL2 between the different species (Dxy) are in the same range, having a mean value of 1.96 and 2.00%, respectively (Table S5).
The levels of divergence of these loci between the different species were low as well.
The present results showed shallow levels of divergence among the members of the P. imbricata/ fucata/ radiata species complex, comparable to the levels of divergence of conspecific exemplars of other Pinctada species.
With these data, we compared the families and levels of divergence of units in both regions and interpreted the data in relation to the numbers of rDNA loci and levels of divergence in the intergenic spacer sequences (IGS).
For levels of divergence of ~1% Sawyer's test has been shown to have at least equivalent power to a number of other methods for detecting gene conversion [ 17].
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