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The method implemented in BEAST [44], [127] simultaneously estimates divergence times, tree topology and rates, thereby providing a clear advantage over previous relaxed clock methods [128] that estimate tree topology and divergence dates separately [129] [131].
This program simultaneously estimates divergence time, time to most recent common ancestor, effective population sizes of the present-day lineages and their ancestor, the proportion of the ancestral population that has founded one of the descendant populations (to account for changes in population size), as well as pairwise migration rates, under the coalescent model [34].
According to mitochondrial DNA TMRCA estimates, divergence among lineages is estimated to have occurred since the Early Pleistocene.
Table 1 shows additional statistical phylogeography metrics including the Kullback Leibler test that estimates divergence of prior and posterior probabilities of the root state.
This approach estimates divergence with correction for polymorphisms segregating within lineages and alleviates the effect of an apparent acceleration of the rate of recent sequence evolution due to segregation of deleterious polymorphisms [ 54].
The method implemented in BEAST simultaneously estimates divergence times, tree topology, and rates, thereby providing a clear advantage over previous relaxed clock methods [ 39] that estimate tree topology and divergence dates separately [e.g. [ 40- 42]]).
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The analysis used the ITS2 topology obtained from the divergence estimation (see Estimating divergence times ).
We estimated divergence times using the Bayesian relaxed clock method calibrated with node ages from previous studies.
These methods all estimate divergence times very similar to Zuckerkandl and Pauling's original conception of the molecular clock.
This approach to estimating divergence times was recently applied by Song et al. (2015) to the evolution of the Orthoptera.
Estimating divergence time is useful to reconstruct evolutionary history.
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