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Recently, Boussau et al. [ 51] established a BD phylogenetic model for co-estimating gene and species trees without the need of estimation of divergence times in species trees and duplication and loss rates.
In order to overcome the limitations of conventional estimates of divergence time based on FST values (e.g. estimation of divergence time assuming isolation without gene flow) [ 75- 77], we employed a coalescent-based MCMC simulation to estimate the divergence times for the main mitochondrial lineages in the program IM [ 78, 79].
We approximated the estimation of divergence by assuming a Poisson solid.
On the other hand, estimation of divergence and rotation by seismic gradiometry, newly proposed in this study, is not restricted by assumptions about wave behavior.
In the estimation of divergence by seismic gradiometry, we used an approximation of Eq. (5) by assuming a Poisson solid to mimic the real-world situation, in which the true inhomogeneous medium is unknown.
The first important question is to what extent the number k of local clocks can affect the estimation of divergence times.
The estimation of divergence times using Bayesian analysis with relaxed clock model suggests a much more rapid speciation process in Hylobates than in Nomascus.
We evaluated whether the estimation of divergence times at three specific nodes were sensitive to the calibration points used by utilizing a jackknife approach.
Although our demographic model does not aim to infer a definitive history, it is important to consider how inclusion of non-equilibrium processes may affect estimation of divergence times.
Strict and relaxed clock models are used in Bayesian estimation of divergence times.
Molecular dating did not allow estimation of divergence times between minor gene pools.
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