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Recent research [88] has suggested that the IR model is more appropriate than the correlated-rates model for divergence time estimation [88].
Finally, our results are not consistent with the model for divergence after duplication [ 2], in which selection continuously favors both the maintenance of the duplicated copies and the divergence of one copy from the parental one.
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Future research should research toward explicit models for divergence in intron exon structures among large sets of metazoans, to allow for systematic prediction of intron functionality across lineages and loci.
These results demonstrate that selection of sequence data appropriate for the time scale of inferences is as important as the selection of calibrations and molecular clock models for divergence time estimation.
This observation suggests that the 8% divergence criterion we used as null model for evolutionary divergence is likely too low and also suggests that our power for many regions was inadequate due to the small number of TFBS or miRNA target sites identified (see above).
The widely used model for estimating divergence times was based on the assumption of correlated rates between ancestral and descendant lineages.
This leads us to propose a model for the divergence of LVS and FTNF002 from the more ancestral OSU18 (Fig. 3).
The mathematical calculations provide the conceptual foundation for the method and predict its performance given a basic evolutionary model for sequence divergence.
We confirm that the rest of the Csl families have a different evolutionary origin than CslA and CslC, and have proposed a model for the divergence order among them.
Recently, Heath et al. [ 103] introduced the fossilized birth death process, a model for calibrating divergence time estimates in a Bayesian framework, explicitly acknowledging that extant species and fossils are part of the same macroevolutionary process.
To elucidate the divergence processes in gibbon evolutionary histories, we analyzed our multi-locus sequence data using two coalescent-based approaches: the reconstruction of a species tree and the isolation-with-migration (IM) model for population/species divergence.
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