Numbers indicate the percent of bootstrap support for the splits obtained after 1,000 replicates.
The bootstrap support for the Wheelwright clade in the Parsimony analyses was 63 (supplemental Figure S2).
Bootstrap support for the NJ tree was low (61) and thus this gene was unlikely to have experienced recent LGT.
However, bootstrap support for the grouping of anthox6a with Gsx is very low; the bootstrap proportion (BP) is only 0.04.
If this sequence is eliminated, bootstrap support for the Plant II subfamily is much higher (e. g. 92% of support in neighbor-joining analyses).
One striking feature of all phylogenetic trees analyzed in this study was the poor bootstrap support for the Chlorobi and Bacteroidetes lineages.
However, the bootstrap support for the groupings within fish taxa for PDGFRβ1 was relatively low (54 69%), therefore this tree is not presented.
We used RAxML to infer the trees and used both RAxML (100 replicates) and PHYML (200 replicates) as described above to infer bootstrap support for the nodes in these trees.
Because of the short lengths of paralogous alignments and overall conservation of the defining domain of CPR proteins, bootstrap support for the monophyly of these groups is usually low.
Bootstrap support for the unweighted MP tree suggests expected species-group support (e.g., C. dalli and C. challengeri grouped with 97% bootstrap support) but very little resolution at deeper nodes of the tree (similar results with NJ).
For each tree along the alignment 1000 bootstrap replicates are generated and the bootstrap support for the clustering of the query sequence with each of the pre-defined parental groups is recorded.
