Although 16S rRNA is the commonly used sequence to study evolutionary divergence, some discrepancies between the rRNA trees and gene trees in the investigation of individual genes and proteins have been previously discussed [ 32, 33].
Significant differences in synonymous substitutions rates among the gene groups indicate the role of neutral substitutions in driving the evolutionary rate discrepancies among them.
Model A: Genome diversity was characterized by the discrepancy of evolutionary distance on phylogenetic tree.
It is possible that the discrepancy among evolutionary rate estimates for RHDV is partially attributable to variation among datasets (uneven temporal or geographic representation, number of taxa, portion of genome analyzed) and/or subtle methodological variations [ 34- 36].
Separate ratios of nonsynonymous to synonymous substitution rates for external (ω e ) and internal (ω i ) branches were estimated using HyPhy This important discrepancy in evolutionary rates between those AIV subtypes that circulate in wild birds compared to poultry can be explained in at least two ways.
Encountered on different evolutionary time scales, this discrepancy may be resolved by taking into account the probability of intra-individual fixation of mutations present in heteroplasmy, and the sex of individuals carrying a new mutation, since males will not transmit them [ 29, 30].
The discrepancies in evolutionary rates along different lineages are not excessively large, however.
This discrepancy in the evolutionary pattern could be due to several factors.
However, metapopulations are also precisely the sort of ecological backdrop for which one expect discrepancies between the evolutionary outcomes derived from clonal reproduction and diploid genetics, because substantially many mutant homozygotes appear locally even though the mutant is rare globally.
We found significant evidence of type I functional divergence for comparisons between different gene clusters (θ I = 0.23 ~0.40, P < 0.01; Table 3); namely, there were some amino acid sites with discrepancies in their evolutionary rate between these paralogous pairs.
