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The introduction of the variable time in the phylogenetic analyses allows to identify variations of the evolutionary rates in different taxa.
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The implications of increased variation on the evolutionary fate of SDs are largely unexplored.
Part of the variation of the evolutionary rates can be explained by fluctuations in finite samples.
However, heterotachy, i.e. variation of the evolutionary rate of a given position over time, is now commonly used as a source of functional information.
Thus, differences in the number of interaction partners seem to explain, at best, only a small part of the great variation of the evolutionary rates of proteins encoded in each genome [ 11].
Recent methodological advances in molecular dating have aimed at relaxing the assumption of the global molecular clock [ 30] by modelling the variation of the evolutionary rate along the phylogenetic tree [ 31- 35].
Heterotachy (covarion) is define as the variation of the evolutionary rate within a given site, and it was shown to have an impact on phylogenetic inferences [e.g., [ 71]].
The estimated variation caused by sampling error positively and significantly correlates with the observed variation (rS = 0.59 and rS = 0.64 for P1 and P2 data sets, respectively; P< 0.0001 for both data sets) but was insufficient to fully explain the dependency of the variation of the evolutionary rate on the alignment length and the COG-specific evolution rate.
Taken together, these results indicate that the extreme variation of the evolutionary rates of core prokaryotic genes detected in this work is a robust observation that is not due to artifacts of either alignment methods or of methods employed to estimate the evolutionary distances.
We introduce new high level reactive search strategies based on a generic algorithm's controller that is able to schedule the basic variation operators of the evolutionary algorithm, according to the observed state of the search.
The observed wide range of local variation of the relative evolutionary rates might cast doubt on the very validity (in a sense, the very existence) of gene-specific relative evolution rates.
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