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Thus, considering the maximum parsimony principle (Ockham's razor), the QuBiLS-MIDAS approach seems to be more suitable than the other QSAR methods.
If the ancestor Y. pestis strain was DFR12 positive, genomovar14 and strain Angola must abandon DFR12 from their genomes again, which can not be well explained by maximum parsimony principle in the evolution.
The estimation of nucleotide substitution directions in the three species by the maximum parsimony principle.
Toward this end, we employ a simple idea based on the maximum parsimony principle.
We determined gain and loss of overlaps using the maximum parsimony principle [ 32] and the species tree.
The maximum parsimony principle suggests that a given set of xor-genotypes should be explained by the smallest number of distinct haplotypes.
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Moreover, based on the maximum-parsimony principle and using three or more species for which the phylogenetic relationship is evident, we can estimate the occurrences and the precise directions of evolutionary changes (such as rate acceleration or deceleration) on each lineage.
When three species, for example S. paradoxus, S. mikatae and S. bayanus, have five members in a certain gene family, whereas only four genes in the corresponding S. cerevisiae gene family, we can estimate a paralogous gene loss in the lineage leading to S. cerevisiae (lineage A) based on the maximum-parsimony principle.
As shown in Figure 2, based on the maximum-parsimony principle, we found that the rates of protein evolution of 7, 52, 22, 24 and 34 genes were accelerated in the lineages A, B, A-B, A-B-C and D, respectively.
Fig. 1 This figure illustrates inferring evolutionary history with the principle of maximum parsimony: a) DNA alignment (substitutions highlighted), b) the most parsimonious tree topology (inferred synapomorphies are in bold; homoplasies are boxed), c less parsimonious topology.
To deal with this, we rely on the principle of maximum parsimony.
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