With the advent of genome sequence data, researchers studying the molecular phylogenetics of bacteria realized how common prokaryotic horizontal transfer is [ 11, 12].
An additional difficulty in naming transposable elements results from the common occurrence of horizontal transfer.
Similarly, the gnd sequence of Rhinoscleromatis isolates (alleles gnd-42, gnd-45 and gnd-46) were either identical or highly similar (Figure 2) to those of K. pneumoniae K3 isolates (gnd-42, gnd-43 and gnd-44), demonstrating their recent common ancestry and their horizontal transfer into distinct genomic backgrounds.
To account for the rare occurrence and dispersed distribution of the rare forms of SerRS and ThrRS, we propose that the rare forms of these two enzymes diverged early from the common forms, with subsequent horizontal transfer from an unknown ancient lineage that probably has gone extinct or is yet to be discovered.
It has been suggested that these related bacteria have acquired RmInt1-like elements by vertical inheritance from a common ancestor and by independent horizontal transfer events.
Movement of symbionts and the traits they encode are now known to be very common through both inheritance and horizontal transfer.
The phylogenetic analysis supports the hypothesis that the lysine biosynthetic operon and its cognate lysine riboswitch have been acquired by a common ancestor of Thermotogales via horizontal transfer from a Clostridium-like Firmicute [ 21].
There are three explanations for this broad taxonomic distribution of phototrophic metabolism; it evolved in one lineage of eubacteria and spread at a later time to other lineages by horizontal transfer, the common ancestor of these groups possessed this metabolism and genetic machinery, or there was a combination of horizontal transfer and vertical inheritance [ 4].
It is tempting to speculate that the rearrangements observed amongst DNA MTases but not other MTases are induced [ 5] by the increased exposure of their genes to the repertoire of various nucleases encoded by different hosts during horizontal transfer events common among the RM systems (J. Elhai, personal communication).
This inconsistency between the current phylogeny including AA1_3 and the traditionally-accepted phylogeny of A. delicata poses a number of questions. A. delicata is one of the earliest branching Agaricomycete lineages, meaning that AA1_3 could either have been inherited and conserved from a common ancestor or acquired by horizontal transfer [ 62].
