Classifying the genera of tribe Zonariae based on these morphological and anatomical characteristics is basically agreed to five clades in phylogenic analyses based on gene sequences.
Phylogenetic analyses based on gene order (fig. 3 A and B) were ambiguous.
This combination method was applied in all other presented analyses based on gene p-values if not indicated otherwise.
In contrast, analyses based on gene co-expression algorithms perform well across data types [ 7] and inspire working hypotheses since their results resemble hierarchical signaling networks.
Wahlenbergia is the sister to these three taxa in all analyses with varying levels of support (BS = 82, 60, 69, 99, 99, in the five analyses based on gene order changes).
Conventional data analyses based on gene-by-gene statistical evaluation of differential expression can often miss this type of informative coordinated regulation of relevant sets of genes, because the fraction of genes individually satisfying the stringent threshold set to define statistically significant changes in expression is too low.
The extent of gene rearrangement within such an evolutionarily young group offers the opportunity to explore gene dynamics such as tRNA remolding, which appears to have been rife within this family, and to investigate its consequences for phylogenetic analyses based on gene orders.
Despite the key-role of plasmids in the prokaryotic world, the evolutionary dynamics of plasmids have been poorly explored, mainly because of the lack of extensive similarities between them, except for genes involved in replication and transfer functions [ 12, 13], which hampers classical phylogenetic analyses based on gene genealogy and synteny [ 14].
The first hypothesis was supported in phylogenetic analyses based on phytochrome genes [ 3] and 17 plastid genes [ 6] but bootstrap support for a sister relationship of monocots and eudicots was only 67%.
To the extent that this result is more broadly representative, it suggests that phylogenetic analyses based on entire genes may overlook almost half of the gene sets actually affected by within-gene LGT.
