Darwin’s Tree of Life is Numbered. Resolving the Origins of Species by Mass

A new view of the tree of life has been conceived and implemented to construct a molecular-based phylogeny for a wide range of animal species without the need for gene or protein sequences using mass map data in a so-called “phylonumerics” approach. Numerical mass map data generated following the proteolytic digestion of proteins expressed across an array of organisms are used to build phylogenetic-like mass trees using a purpose built MassTree algorithm. The algorithm inputs sets of numbers for each organism and builds the tree, by default, using a relaxed Neighbour-Joining Approach with mid-point rooting. Single point mutations are also uniquely identified from peptide mass differences and these mutations displayed on branches of the mass trees. Here a wide array of animal species comprising insects, fish, birds, land and aquatic reptiles, and large mammals are successfully resolved and correctly grouped according to their origins on such a number-based tree. The mass tree is found to be highly congruent with that generated using sequence data and can be used to study evolutionary pathways at the molecular protein level without sequence generation or alignment. Mass trees provide a useful complement and viable alternative to conventional gene sequence trees. The approach brings together previously disparate fields and provides a universally applicable means with which to represent life forms and their evolutionary history employing a new molecular-based phylogeny that should find widespread application among the evolutionary biology community.