(a) Ancient paralogs 1 and 2 have descended from a common ancestor in the Bacteroidetes phylum (organismal ) following an ancient gene-duplication (Dp) event (depicted with a horizontal bar).
The speciation (Sp) event from which the Sphingobacterales order diverged is represented by an inverted 'Y' lineage. Ortholog combinations (A1 & B1 or A2 & B2) are on lines that meet at
an inverted 'Y', whereas paralog combinations are always on lines that meet at a horizontal bar. This diagram follows the usage of Fitch (Fitch, W.M. 2000. Trends Genet. 16: 227-231.).
(b) The speciation event that led to divergence of upper-Gammaproteobacteria (X) from lower-Gammaproteobacteria (Y) is diagrammed. These lineages have in common an aspartokinase
gene that descended in the vertical genealogy, a gene known as ask_alaS because of its conserved gene neighborhood with alaS. The lower-Gammaproteobacteria have
additionally received via LGT two genes, one of which duplicated to yield two paralogs. Thus, lower-Gammaproteobacteria have three xenolog ask genes that are not present in
upper-Gammaproteobacteria.
(c) The divergence point of the Enterobacterales order from the lower-Gammaproteobacteria corresponds with the loss of the ancestral ask_alaS.
(d) The acquisition by lower-Gammaproteobacteria of the gene encoding the common ancestor of the paralogs encoding thrA and metL was obtained via LGT from some
organism that can be pinpointed to the Sphingobacterales order, as is shown on the lower left. On the lower right is shown the acquisition of lysC by lower-Gammaproteobacteria
from a donor which can only be defined as a member of the Bacteroidetes phylum.
