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There was no difference between different demographic models compared within the UCED clock model (2lnBF <2lnBF
The degree of power reduction differed for different demographic models or values of L. This finding reflects that the power is influenced by the relative magnitudes of changes in allele frequencies at R + 1 loci and sampling errors.
For all tests of neutrality, coalescent neutral simulations were run under different demographic models to assess the significance of the resequencing data.
Approximate marginal likelihoods of the different demographic models were calculated with enforced strict and relaxed molecular clocks (Table 3, 4 and 5).
Four scenarios were simulated combining the two different demographic models described below (CD and DD) for the Neolithic transition with the two alternative hypotheses for selection at LC T*P(gcc and cal).
Our approach combines the evaluation of different demographic models using a best-fit approach, followed by an ABC analysis of the data that conveniently deals with the co-estimation of multiple inter-dependent parameters [45], [46].
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In D. pseudoobscura, a very different demographic model is estimated.
Different parametric demographic models (a constant population size, exponential and logistic growth) and a nonparametric Bayesian skyline plot (BSP) were compared under strict and relaxed clock conditions, and the best models were selected by means of a Bayes factor (BF, using marginal likelihoods) implemented in Beast as already described [ 28].
To test significance of the three different classes of demographic models, we note that the constant size model is a specific case of the two- and three-epoch models, and the two-epoch model is a specific case of the three-epoch model.
We applied a fixed sex ratio and a random mating scheme (i.e. parents are randomly selected irrespective of their genotype) validated by different genetic and demographic models (27).
To confirm WFDC departures from neutrality, we performed 10 coalescent simulations for each subspecies under different demographic scenarios: constant model (P. t. troglodytes, P. t. ellioti, P. t. verus), our best-fit model (P. t. troglodytes, P. t. ellioti, P. t. verus), Hey 2010 model (P. t. troglodytes), and Wegmann and Excoffier 2010 model (P. t. verus).
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