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Phylogenetic trees were inferred using both the maximum likelihood approach as implemented in PHYML 2.4.4 [52] and the Bayesian approach implemented in MrBayes 3.1.1 [53.1.1
Thus CD59 clade was recovered in both the maximum likelihood and Bayesian phylogenies and the network shows that this grouping is well supported by the data.
Phylogenetic reconstruction was conducted using both the maximum likelihood (ML) and the Bayesian approaches.
Two of these groups are monophyletic with significant (≥ 95%) support in both the Maximum Likelihood and Bayesian analysis (Group I and III).
Both the Maximum Likelihood (ML) and Bayesian Inference (BI) methods recovered the subtribe Mycalesina as monophyletic with high posterior probabilities (PP) and strong bootstrap supports (BS).
Results from both the Maximum Likelihood and Bayesian dating analyses have been deposited in TreeBase (http://purl.org/phylo/treebase/phylows/study/TB2 S14458).
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While both the low MDI value and the maximum likelihood estimate of the λ parameter suggest that brain size evolution does not depart from Brownian motion, the maximum likelihood estimate of the α parameter suggests that brain size evolution is possibly better described by an Ornstein-Uhlenbeck model [ 31, 32].
Both the maximum likelihood-based estimation and Bayesian MCMC analyses strongly supported East Asia as the ancestral area of lethal amanitas.
The BMD estimates for TSH were infinite, because in both cases the maximum likelihood estimate of the parameter β was zero.
Regarding the Acsl3 and Acsl4 trees, both in the Maximum likelihood and Bayesian analysis we observe that the invertebrate Acsl-like sequences again out-group two well supported groups containing vertebrates sequences.
Both criteria require an estimate of the maximum likelihood, for which we used the maximum value of the log-likelihood encountered by the MCMC algorithm in the post burn-in period.
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