Column containing gaps were not used in the phylogenetic estimation.
Filtering and subsampling loci using the phylogenetic informativeness method resolves several recalcitrant phylogenetic relationships within Aristolochia.
This is the first application of an ACO algorithm to the phylogenetic estimation problem.
This confirms that these fastest evolving sites may mislead the phylogenetic inference of position of lycophytes, so we used the phylogenetic tree based on OV-sorted data for divergence time estimation.
Phylogenetic trees were generated for comparison of each analysis method; in-house core-SNP pipeline, AMPHORA, 16S rRNA, groEL, and rpoB using Phylogenetic estimation using Maximum Likelihood (PhyML 3.0) [ 121] with nucleotide substitution models LG.
Gene trees were reconstructed using PhyML (Phylogenetic estimation using Maximum Likelihood) [ 50, 51] with the General Time Reversible plus Gamma (GTR + G) substitution model of DNA evolution, and the Subtree Pruning-Regrafting (SPR) branch-swapping method.
The main alternative to supertree methods are combined analysis methods, also known as supermatrix or total evidence approaches; these methods concatenate the alignments on each marker to produce a large "combined dataset", which is then analyzed using a phylogenetic estimation method (e.g., maximum likelihood or maximum parsimony).
We predict that as more genomic sequences become available for other Rickettsia spp., the four clades defined herein using phylogenetic estimation (AG, TG, TRG, SFG) will remain strongly supported, and that R. australis and other rickettsiae with either recent host switches or the presence of plasmids, will likely fall within the AG and TRG rickettsiae.
This cladistic pattern corresponds with the highly distinct N-terminal sequences (which were not used in phylogenetic estimation), providing independent validation of the relationships.
The protocol for analysis of sequence variation is described in Additional file 8. Essentially, after preparation of multiple alignments, the variation among sequences was quantified and characterised using phylogenetic estimation.
