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The second method 'unresolved' the most terminal nodes on the phylogeny.
Thus, unresolving only the most terminal nodes in the phylogeny had much less influence on the power to predict the real NRI and NTI whereas randomly unresolving nodes on the phylogeny had a much greater negative impact.
The loss of predictive power is far greater when the phylogeny is randomly unresolved (Fig. 3, 4, and 5) compared to when the most terminal nodes were unresolved (Fig. S1, S2, and S3).
When 'unresolving' only the most terminal nodes on the phylogeny, the NRI and NTI in the assemblages were generally highly correlated (r2>0.8) with the NRI and NTI values from the fully bifurcating phylogeny (Fig. S1, S2, and S3).
The correlation was slightly weaker for all three metrics of phylogenetic diversity when the phylogeny was randomly 'unresolved' as compared to when only the most terminal nodes were 'unresolved' (Table S1, S2, S3, S4, S5, and S6).
Converse to this pattern, when only the most terminal nodes of the phylogeny were unresolved the slopes from the NRI and NTI regression analyses were near one with small deviations above and below one.
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The branch lengths for the edges subtended by the collapsed node were set to equal the length between the collapsed node and the next most terminal node in each lineage.
The right-most terminal node, T4, has the highest mean concentrations.
While this loss of power is of concern, the results also suggest that if the most basal nodes are bifurcating and terminal nodes are unresolved the loss of power is greatly minimized.
From the scheme in Figure 6, the comparison results indicated that most of duplicated paralog pairs at the terminal nodes of the phylogenetic tree may have maintained their ancestral function.
Specifically, I collapsed 15, 20, 25, and 30 percent of the internal nodes in the phylogeny that were the most terminal on the phylogeny.
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com