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EFL phylogenies were inferred using the same models used for EF-1α.
The observed frequency of TFBSs relative to the start codon and its randomized expectation were inferred using the same method.
This tree was inferred using the same set of concatenated genes used for constructing the species tree but now inference was done based on the nucleotide sequences.
ProML trees were inferred using the same settings, and 100 bootstraps were inferred with the gamma shape parameter alpha and proportion of invariant sites estimated using Tree-Puzzle 5.2 [ 33].
If the method of analysis was the main methodological driver of phylogenetic incongruence, then: (i) morphology-based Bayesian phylogenies should reduce conflict with molecular phylogenies inferred using the same methods; and (ii) the MP morphological phylogeny should share more nodes with the MP molecular phylogeny than with the ML or Bayesian molecular phylogenies.
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The tree was inferred using the MrBayes program and the same alignment as the one used to build the corresponding maximum likelihood tree (Fig. 1 ).
The evolutionary relationships were inferred using the neighbor-joining method.
Orthologs are inferred using the Reciprocal Smallest Distance algorithm.
The phylogeny was inferred using the Maximum Parsimony method as described in the methods.
The most likely K (number of groups) was inferred using the DeltaK criterion50 with STRUCTURE HARVESTER51.
Additional evolutionary analyses of the isolates of interest were inferred using the Maximum Parsimony (MP) method.
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