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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.
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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.
Models for estimating divergence times under a molecular clock have become more complex over the past two decades.
The conserved stress conditions thus provide ideal models for studying divergence and evolvability of gene regulation in evolutionarily distant organisms.
In a first part of the paper, we fit a measure of backbone gene order conservation (hereinafter called backbone stability) against phylogenetic distance for over 3000 genome comparisons, improving existing models for the divergence in time of backbone stability.
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).
We used the program 3s v2.1 (Yang 2010; Zhu and Yang 2012) to test models of divergence with gene flow for each triplet of Sceloporus.
These models are important for divergence time estimation procedures.
The widely used model for estimating divergence times was based on the assumption of correlated rates between ancestral and descendant lineages.
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