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Molecular sequence estimates place the divergence between the two orders around 55 60 Myr ago [ 32, 33, 48].
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Partitioning of the molecular sequence alignment may impact on divergence time estimates [ 56, 57].
Rannala and Yang [ 37] developed a birth-death phylogenetic model for estimating phylogenetic trees from molecular sequence data.
For instance in long-branch attraction types of scenarios where gene trees can not be consistently estimated from molecular sequences, MP-EST may consistently estimate a wrong species tree due to the bias in the gene tree reconstruction.
The posterior estimates of times are then the result of combining the prior (the fossil information) with the likelihood of the data (the molecular sequence alignment).
Estimating divergence times from molecular data is a special statistical endeavor, as the parameters of interest cannot be directly estimated from molecular sequences: only distances between pairs of sequences or site likelihood values can be estimated.
As in the case of episodic evolution, a simple lack of historical signal present in molecular sequences could generate erroneous divergence time estimates.
Such times are usually estimated on the basis of molecular sequences [ 32] and fossil records.
We build on the signal and noise framework of Townsend et al. [ 56], which uses the estimated substitution rates of individual molecular characters to estimate the power of a set of molecular sequences for resolving a four-taxon tree with equal subtending branch lengths.
Assumption of a molecular clock is useful for estimating the divergence time between orthologous molecular sequences.
We found the Bayesian skyline plot a useful method for estimating ancestral population dynamics from our sample of molecular sequences as shown previously [67].
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