  Many methods have been developed for finding the commonalities between
different organisms to study their phylogeny. The structure of metabolic
networks also reveal valuable insights into metabolic capacity of species as
well as into the habitats where they have evolved. We constructed metabolic
networks of 79 fully sequenced organisms and compared their architectures. We
used spectral density of normalized Laplacian matrix for comparing the
structure of networks. The eigenvalues of this matrix reflect not only the
global architecture of a network but also the local topologies that are
produced by different graph evolutionary processes like motif duplication or
joining. A divergence measure on spectral densities is used to quantify the
distances between various metabolic networks, and a split network is
constructed to analyze the phylogeny from these distances. In our analysis, we
focus on the species, which belong to different classes, but appear more
related to each other in the phylogeny. We tried to explore whether they have
evolved under similar environmental conditions or have similar life histories.
With this focus, we have obtained interesting insights into the phylogenetic
commonality between different organisms.
