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However, the median evolutionary rate in the two HIV-negative subjects with chronic HCV infection was 10 times lower than that in the HAART-treated subjects (0.29×10−3 sub/site/month), and the relative evolutionary rate at codon positions 1st+2nd was between 1.4 and 5.5 times lower than that at codon position 3rd (Table 4).
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Given the simulation results, we predicted that pile-weave design characters would exhibit higher median evolutionary rates than the other textile characters if they had experienced more independent horizontal transfers as peripheral elements of a hierarchically integrated system.
We also used Tajima's relative rate test (Tajima 1993) to compare the nucleotide substitution rates among Pinaceous genera using generic representatives that have median evolutionary rates (supplementary table 4, Supplementary Material online).
To confirm that our APC ncRNAs are more conserved than NL ncRNAs, we calculated percentage identity and median genomic evolutionary rate profiling (GERP) scores (GERP method, Cooper et al. 2005) from the genomic alignment.
However, we did not find a significant result for the TF-miRNA pairs that are connected by transcriptional repression signals (median miRNA evolutionary rate: 0.042 vs. 0.037, P = 0.5, Wilcoxon test, Figure 2B).
Though, our data for evolutionary rate scattered broadly, the median evolution rate of the TFBSs in our dataset, is significantly higher at NRs (0.45) than at NDRs (0.37) according to Wilcoxon-Mann-Whitney U two-sample test (p-value = 1.61×10-32).
We found that targets in the low rate group had a higher evolutionary rate than those in the high rate group (median dN: 0.052 vs. 0.046, P = 0.02, Wilcoxon test).
In the strict clock model, the evolutionary rate estimates were similar in group A and B (median values respectively 1.9 and 2.3×10−3 sub/site/month); the estimate was significantly lower than in all of the other coinfected subjects in one group B subject (#7 again): 0.17×10−3 sub/site/month (95%HPD 0.03-0.3×10−3) (Table 4).
For the 570 orthologs analyzed, the fold-increase in evolutionary rate along the lineage leading to B. vafer had a wide range (0.1 - 4.6), but a median value of 1.04, indicating no systematic rate difference between the B. vafer and B. floridanus lineages (Additional File 2).
"Evolutionary rate at the molecular level".
The degree of evolutionary conservation was scored by Genomic Evolutionary Rate Profiling.
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