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Most nodes show high posterior probabilities, yet, several shallow nodes of our mitochondrial and nuclear trees are only weakly supported.
In contrast, scale-free systems are relatively resistant to perturbations because most nodes show only limited connectivity.
The topology remains the same when the 3rd codon position of the COI is excluded from the data set, but most nodes show lower posterior probabilities or likelihood values, respectively (Additional file 1).
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Evidence from genome sequencing and known biochemical functions of specific proteins suggests that specific nodes within biologic networks show high degrees of connectivity to other components ("hubs"), while most other nodes show low degrees of connectivity [ 27].
The hot (reddish) edges incident to the largest nodes show where these differences manifest most strongly, i.e., which other nodes are discriminated by such a node (and its cluster) by moving from treatment one to treatment two.
In any case, however, we observed that most nodes of our TRNs exhibit a low connectivity, while very few nodes show a very high degree.
Second: Nodes show preferential attachment.
Dodson et al. reported that the total amount of asbestos in the lung was quite low, whereas most cases having asbestos in the lymph nodes showed larger amounts of asbestos in the nodes than in the lung [ 23, 24].
When taken separately, the exclusion of fast evolving sites for introns negatively affected the support for most nodes (data not shown), whereas, when concatenated, all of them (to the exception of the grouping D-Myomorpha+Anomaluromorpha) are strongly recovered (see Table 4 and Additional file 4).
Surprisingly, most of the histologically negative, but immunohistochemically positive, lymph nodes showed high CK19 mRNA value.
Two nodes showed a decrease in net diversification: the base of Thomasomyini clade and the most recent common ancestor of Reithrodon-Irenomys (nodes 91 and 84 respectively, see also Additional file 5: Table S5).
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com