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Brandley et al. [34] demonstrated that accommodating different rates of evolution among subsets of DNA data may improve divergence time estimation, especially when different subsets of the data evolve at different rates.
Finally, extensive analyses of this data set have demonstrated that the use of models that account for rate heterogeneity among subsets of the DNA dramatically improve divergence date estimates and help mitigate potential problems inherent in using distantly related age calibrations [34].
This means that for a given set of calibration information, simply augmenting the number of sequences would not be sufficient to improve divergence time estimates.
MtDNA may have further utility in making progress on the problem, as our analysis of posterior credibility interval widths indicates that longer sequences would likely improve divergence time estimates.
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Although the present study has yielded improved divergence time estimates, it is possible that the estimates of the time of origin for some genera such as Ottelia, Vallisneria, Najas and Blyxa may have been affected by under-representation in sampling.
As it moved towards the west and subsequently southwards, improving upper air divergence allowed the system to intensify, reaching tropical cyclone intensity on the evening of 11 December and thus attaining the name John.
We also examined whether more sequence data would improve our estimates on divergence times by plotting the posterior means of divergence times against the width of their corresponding 95% credibility interval (see Additional File 1, Figure S3), following Yang and Rannala [ 22].
Despite this pattern, sampling additional populations from each region would likely improve estimates of population divergence and assignment accuracy.
The S. arboricolus genome sequence should enhance the power of comparative genomics by increasing the total sequence divergence and improve the quality of alignments by adding a new branch between S. bayanus and S. kudriavzevii, the more divergent species.
Events of regular sound change can provide strong signals preferring some phylogenetic placements over others and can improve the estimation of divergence times over the sporadic-change-only model, which will routinely overestimate the amount of independent change by assuming that each phonemic substitution is independent (Box 1).
A simulation study by Vijay et al. [ 59] demonstrated that reference genomes with average nucleotide sequence divergence up to 15% can help improve transcriptome assemblies while with greater divergence there was no improvement over a de novo assembly.
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