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Since the training set is fixed, the likelihood and evidence densities are in fact time invariant.
Under a fixed, the likelihood ratio test function that maximizes the PD under the NP criterion is (14).
The problem is well-posed in the sense that if J is fixed the likelihood is bounded and can be maximized.
Moreover, if we fix the population sizes for the populations other than Δ in the species tree, it follows from (3) that when the population size θ i is fixed, the likelihood of population i is always greater than a positive number, because b i in (3) is bounded.
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For the tree of [ 47], we made the representation of organisms non-redundant at the genus level, with a small number of exceptions for fast-evolving genera, and recomputed the best Maximum Likelihood tree, while keeping fixed the original topology of the published tree ('constraints' in RAxML).
To identify codon sites under positive (adaptive) or negative (purifying) selection, we used the single-likelihood ancestor counting, the fixed effects likelihood and the random effects likelihood methods.
We made separate analyses with the fixed effects likelihood methods (FEL and iFEL) and with the random effect likelihood method (REL) (Pond and Frost 2005).
The dN/dS ratio among codons was calculated using the maximum likelihood method with the codeml program in PAML 4.5 [ 35, 36], as well as the fixed effect likelihood (FEL) method implemented in HyPhy (version 0.99b) [ 37].
What factors determine the likelihood that a particular rearrangement becomes fixed in a population?
For these purposes, we estimated survival rates of young by fixing the beta parameter in the likelihood function estimated for the covariate "use of AFS" to 0 (see results).
In the GLMM, the Wald statistics are recommended to test the null hypothesis of fixed effects because the likelihood ratio tests are unreliable for small to moderate sample sizes [ 8- 10].
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