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Since intra-patient recombination would lead to the creation of mosaic genomes violating the tree-like assumption of evolution, we carefully checked for recombinant sequences within our data sets before performing high-resolution phylogenetic analysis.
Ultimately, all diagnostic tests of our correlation analyses were insignificant, indicating our data met the assumption of evolution under a Brownian model.
We think that the number of the members of the respective subgroups, the distribution of Q2-2 and Q2-3 as well as the distribution of non-finger conserved motifs favor the assumption of evolution from a low number to a higher number of domains and not vice versa.
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Fig. 5 Visual illustration of the three assumptions of evolution by natural selection.
Yamanoi (2008) reported that even after the origami bird experiment with the original protocol, Japanese high school students who had studied evolutionary concepts failed to understand the three assumptions of evolution by natural selection.
Although standard models of nucleotide evolution violate the assumption of independent evolution of all sites when also applied to paired sites as done by Redmond et al. [ 41], this seems to have little impact on nodes with high support values in the case of the demosponge dataset studied (compare Fig. 1 in [ 41] with our Fig. 5).
The co-evolution of doublets violates the assumption of independent evolution of sites made by most phylogenetic methods [ 7].
Therefore, to mechanistically model the evolution of protein sequences, these residue-residue interactions must be considered, relaxing the common assumption of independent evolution of each amino acid position [ 2].
Trends in the comparative study of religions have retained the interest in morphology but have decisively rejected the almost universal 19th-century assumption of unitary evolution in the history of religion.
The sequences of an MSA, however, fail to meet the assumption of independent evolution.
MI is also affected by various sources of bias, because the sequences in a MSA do not exactly meet the assumption of independent evolution.
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