Reimaging the Tree of Life Using a Mass Based Phylonumerics Approach

Evolutionary relationships among and across species are almost exclusively examined through phylogenetic analysis based on trees constructed using gene sequences. Such trees are not without their limitations. Here we show that sets of numbers representing the masses of peptide segments within proteins encoded by those genes can also be used to construct trees of life employing a phylonumerics approach. A purpose built algorithm developed in this laboratory has been used to construct so-called mass trees from these numerical mass map datasets for hypothetical proteins encoded by the 16S/18S gene across all forms of life. A mass and conventional sequence tree built from 736 proteins across all six kingdoms of life (comprising 201 animals, 26 plants, 12 fungi, 13 protists, 236 archaea and 248 bacteria) show considerable similarity and demonstrate the broad viability of a phylonumerics approach for displaying and studying biodiversity and evolutionary history. A visual and computational comparison of mass trees and conventional sequence based trees, using several tree comparison algorithms, demonstrates that the former represent a reliable and effective means to study organismal evolution without the need for gene or protein sequences nor their alignment. The phylonumerics approach can also display mutational differences along the branches of these trees to allow for the study of molecular mechanisms that drive evolutionary change.