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For data matrix 3 (exons), the polymorphism and divergence module of the DnaSP package [ 48], using the sliding window option, were used to make a graphic representation of the pattern of change of d N / d S ratios along the sequence.
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The regulatory divergence of Module 5 genes during the evolution of aerobic fermentation could be due to changes in trans-acting factors or in cis-regulatory elements.
Therefore, with respect to the HAP complex, no significant changes in the trans-acting factor or cis-regulatory elements were associated with the expression divergence of Module 5 genes during the evolution of aerobic fermentation.
While a similar proportion (54%) of those that diverge do so as early as they arise, they continue to contribute significantly to the divergence in module assignment at later points compared to non-duplicated genes.
For other two nodes found to be important and had similar divergence between modules, similar differential connectivity was calculated, and relationship to clinical variables was also evaluated.
(G ) Module divergence scales with phylogenetic distance.
We defined two metrics for measuring module divergence: the Module Contraction Index (MCI) and the Module Expansion Index.
This within/between module divergence of frontal nodes was positively correlated with the duration of epilepsy.
It is worth noting that in Osteichthyes, in which zebrafish belongs, regulatory module divergence and subfunctionalization between paralogous genes are common phenomena [ 41].
The knowledge on the nodes of origin, frequency and combination of functional modules in proteins, functional versatility and the degree of divergence of these modules will provide better understanding of the evolutionary solution to the increased complexity of human proteome.
We propose that the divergence of coexpression modules among breeds under positive selection eventually regulated the muscle phenotype divergence during domestication.
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