A new phylogenetic strategy simplifies the problems of character independence. (a) The canonical paradigm explores the evolution of systems, such as the evolution of organisms in the reconstruction of ToLs. For example, the terminals of phylogenetic trees can be genes sampled from different organisms (e.g., Pyrococcus furiosus (Pfu), Methanococcus jannaschii (Mja), and Methanosarcina barkeri (Mba)), and phylogenetic characters can be amino acid sequence sites of the corresponding gene products. Character states can describe the identity of the amino acid at each site. Since characters are molecular parts that interact with other parts when molecules fold into compact 3D structures, their interaction violates the principle of character independence. Consequently, the effects of covariation must be considered in the phylogenetic model used to build the trees. (b) The new paradigm explores the evolution of parts, such as the evolution of protein domains in proteomes. For example, the terminals of phylogenetic trees can be domains defined at fold superfamily level of structural complexity and the characters used to build the trees can be proteomes. Character states can be the number of domains holding the FSF structure. Since proteomes interact with other proteomes when organisms establish close interactions, interactions that could affect the abundance of domains in proteomes should be considered negligible (unless there is an obligate parasitic lifestyle involved) and there is no need to budget trophic interactions in the phylogenetic model.
