A Complex Network Approach to Phylogenetic Trees: From Genes to the Tree of Life

PhD thesis public defense.
Supervisors: Emilio Hernández-García, Víctor M. Eguíluz and Carlos M. Duarte.
Abstract:
The increasing interest during the last century in the study and
comprehension of the evolutionary processes that govern biodiversity,
together with the huge expansion that the complex network approach
has undergone in the last decade, has motivated us to address the
interrelation of both scientific fields. In that sense, within the context
of complex network theory, the main purpose of this work has been
to provide new tools for the topological characterization of evolutionary
trees, as well as to contribute to enlarging the knowledge of the
evolutionary patterns depicted in them. Thereby, we have proposed
an approach based on the depth scaling analysis of phylogenetic trees
in order to carry out comparative studies between micro- and
macroevolutionary phylogenies, gene and species evolutionary trees,
as well as a comparative study of the effects of the rank-based and
rank-free taxonomic criteria over the topology of evolutionary trees.
Besides, we have examined the information stored in the branch
length of the phylograms, in order to characterize the branch length
distribution along the Tree of Life.