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Another important issue highlighted is that with short time series, a small variation in the pre-processing procedure might yield large differences in the inferred networks.
The phylogenetic trees inferred using the MLST data (Figure S1) and RA data (Figure S2) show some striking differences in the inferred relationships among strains.
We compared 20 random families using PROML and NEIGHBOR, and did not find any differences in the inferred tree topologies.
We found no significant differences in the inferred initiation probabilities when artificially doubling the lengths of all transcripts (Kolmogorov-Smirnov, p > 0.9).
Therefore, it is not surprising that slight differences in the data set and in the statistical analyses can yield significant differences in the inferred parameters.
Despite these differences in the inferred decision rules, we found rather similar behaviour at the flock level for the two numerically dominant species: this similarity seems to result from differences in mean abundance for these two species.
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So, can the difference in the inferred amplitude of the hydrology signal be due to the difference in the value of (1/alpha ) used?
If the value of (1/alpha ) is not the main cause of the difference in the inferred amplitude of the hydrology signal in the Nelson River basin, what else can be the cause?
The similarity of these values among the samples of rodingitized felsic intrusive rocks and slates suggests that the difference in the inferred internal pressure of type 2a and type 2b inclusions is not due to large variations in the proportion of the volatiles, but is real.
Although this is probably a reasonable first approximation, more complicated dynamics for a significant fraction of nonsynonymous mutations, such as population structure (local adaptation), balancing selection or very weak positive selection, may have obscured a difference in the inferred efficacy of selection on nonsynonymous sites in the two species.
However, there are a number of key differences in both the inferred demographic model and the corresponding DFE.
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Since I tried Ludwig back in 2017, I have been constantly using it in both editing and translation. Ever since, I suggest it to my translators at ProSciEditing.

Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com