In order to correlate phenotypes with genomic differences we performed detailed analyses of virulence-associated genes that allow us to present hypotheses on the evolutionary descent of these changes (Additional file 12).
Authors' response: In the original abstract where we said "predominantly vertical lines of descent" and in the introduction where we said "the mostly vertical evolutionary descent of a coherent biological entity" with respect to the ribosome phylogeny scaffold, we were anticipating that a ribosome would prove to be rarely transferred for the reasons discussed below.
The recognition of time would eventually lead to the recognition of evolution as a fact of nature, and subsequently, tree iconographies would come to represent exclusively the evolutionary descent of species.
Given the evolutionary descent of mitochondria from bacterial symbionts, one might again learn some lessons from mitophagy.
In bioinformatics, it is mainly used in constructing the so-called phylogenetic tree, which is a diagram that depicts the lines of evolutionary descent of different species, organisms, or genes from a common ancestor [ 5].
The eBURST program was used to assess the genetic relationships of genotypes, to assign isolates to genetic complexes, and to study patterns of evolutionary descent of isolates within a complex (25).
Also Erdmann and Schliebs [ 18] have recently linked the homology between AAA+ domains of ERAD and PEX1, and the presence of E2 and E3 domains involved in ubiquitinylation in the PEX proteins, to a mechanism of protein import in the Peroxisomal matrix that would be similar to ERAD, without proposing a direct evolutionary descent of Peroxisomal import from ERAD however.
The most likely patterns of evolutionary descent in the collection were assessed using the eBURST algorithm (http://eburst.mlst.net), using previously validated parameters [15].
Here, we test whether the architectures identified in the genomes are of evolutionary descent, consistent with low probabilities of convergent evolution [ 16], or whether the PWWP domain has become promiscuous independently in different lineages and, thus, consistent with convergent evolution [ 17].
Where there is disagreement, it relates not to the fact of evolutionary descent but to specific points about the mechanisms, locations, or timing of change.
