Although the basal nodes were not supported in the maximum likelihood reconstruction, the position of these two sequences in the phylogenetic tree and the analysis of their genomic context (Fig. S3 in additional file 3) strongly suggest that they belong to the Pho cluster of orthologs.
However, it is to be noted that orthologous groups of subtilisins inferred by Inparanoid/QuickParanoids [ 38, 39] are not supported by the maximum likelihood-based phylogenetic inference (Fig. 3), suggesting that the similarity-based method of Inparanoid/QuickParanoid should be taken with caution.
This scenario is supported since GH 48 proteins in each insect associated family formed their own supported clusters in the maximum likelihood tree.
Additionally, Groups 5 and 6 form a well supported clade in the maximum likelihood analyses, suggesting that they likely evolved from a common ancestor by frequent gene duplication.
Supports from the maximum likelihood analyses were comparable to the Bayesian analyses.
The branch support of the Maximum Likelihood tree was evaluated by the bootstrapping method with 500 replicates in PhyML.
Statistical support for the maximum likelihood inference tree was evaluated with a non-parametric bootstrap test with 1,000 re-sampling events.
To compare statistical supports of the Maximum Likelihood topologies with alternative placement of caryophyllales as i) basal to both rosids and asterids or iii) sister group of rosids, we generated alternative topologies using ETE v2 [ 84] and their likelihoods were computed for the same alignment with the same parameters.
While all three putative transfers involving eukaryotes show strong support from both analyses and most likely represent true cases of LGT, two of the suggested intra-domain eubacterial transfers and both the prokaryotic inter-domain transfers show only weak support from the maximum likelihood distance analysis and therefore should be viewed as more tentative cases (Figs. 1 & 2).
The relationships of OsYSL1 with other OPT genes, however, cannot be confidently determined in our analyses: OsYSL1 was basal to a large clade consisting of Groups 2-6 weak weak support in the maximum likelihood analyses, but formed a clade with Group 1 in Bayesian analyses.
