  It is proposed that the co-expression of statistically significant motifs
among the sequences of a proteome is a phylogenetic trait. From the
co-expression matrix of such motifs in a group of prokaryotic proteomes a
suitable definition of a phylogenetic distance is introduced and the
corresponding distance matrix between proteomes is constructed. From the
distance matrix a phylogenetic tree is inferred, following a standard
procedure. It compares well with a reference tree deduced from a distance
matrix obtained from the alignment of ribosomal RNA sequences. Our results are
consistent with the hypothesis that biological evolution manifests itself with
a modulation of basic correlations between shared peptides of short length,
present in protein sequences. Moreover, the simple procedure we propose
reconfirms that it is possible, sampling entire proteomes, to average the
effects of lateral gene transfer and infer reasonable phylogenies.

Molecular Networks;Genomics;Populations and Evolution