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However, the within group divergence of Clusters 1 and 3 were only 0.1%and0.2%2%, respectively.
When two methods to estimate LTR divergence as a measure of the insertion time were compared, a deviation in the LTR divergence of clusters of retroviral copies was detected, adding new concerns regarding the use of LTRs to estimate the insertion time of ERV copies, that is, the violation of the molecular clock.
A 203 nt region corresponding to the nucleoprotein gene located between nucleotide 109 and 311 of the PV strain was analyzed as this locus has been employed to demonstrate association with the phylogenetic divergence of clusters in previous phylogenetic studies [ 11, 21].
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We observed a divergence of cluster scores.
This finding supports the notion that the mutation was obtained upon the divergence of cluster P2.
From the 16S*-23S* 16S*-23S*ence diverDNAce of Portiera (the primary endosequence of whiteflies) andivergencemated rate of endosymbiont sequence change [ 24], it is Portiera theestimate the time of divergence of cluster C and the two Aleyrodes sprimary
Thus, the comparison of the divergences of clustered ERVs could be helpful in this scenario.
These results are consistent with the current complement of TRM clusters in opossum being the result of whole cluster duplications followed by divergence of each cluster.
The divergence of this cluster with consensus IV ranged from 1.2% (Cam_318) to 2% (Ov_41).
All six R86 strains have the S315T mutation in katG, explaining the isoniazid resistance, and suggesting it was acquired prior to divergence of this cluster.
We also found evidence of functional divergence of the HoxB cluster from the protoHoxACD cluster after the initial duplication event predicted under the (B(A CD))) model (θI = 0.221 ± 0.07, p < 0.05; Figure 3).
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