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The maximum likelihood used in our study was pioneered by Bhargava and Sargan in their study (1983), which incorporates all of the restrictions implied by the model in an optimally efficient way.
Indeed, neglecting this latter aspect of variability by performing simulations with point estimates (such as maximum likelihood) used as true parameter values could also bias the detection of natural selection.
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Parameter estimation is done by maximum likelihood using first-passage time probabilities of diffusion processes [25].
The three models have been estimated by maximum likelihood using the equations given in Section 3.4.
The phylogenetic tree was created by the method of maximum likelihood using the PhyML (HYK85 model) with 100 bootstrap replicates.
The phylogenetic analysis was conducted by the method of maximum likelihood using PhyML with 100 bootstrap replicates.
The estimation method was maximum likelihood using the covariance matrix according to the suggestions of Hair et al. (2010).
Odds ratios (ORs) were estimated by maximum likelihood using unconditional logistic regression.
The random-effects Poisson model was fitted via maximum likelihood using the xtpoisson command.
Ancestral sequences were reconstructed by maximum likelihood using the software PAML v4 [23].
The combined nucleotide sequences were also analyzed under maximum likelihood using Bayesian inference with the program MrBayes v3.1.2 [205], [205].
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