Phylogenetic Trees and Networks Reduce to Phylogenies on Binary States: Does it Furnish an Explanation to the Robustness of Phylogenetic Trees against Lateral Transfers?

Abstract

This article presents an innovative approach to phylogenies based on the reduction of multistate characters to binary-state characters. We show that the reduction to binary characters’ approach can be applied to both character- and distance-based phylogenies and provides a unifying framework to explain simply and intuitively the similarities and differences between distance- and character-based phylogenies. Building on these results, this article gives a possible explanation on why phylogenetic trees obtained from a distance matrix or a set of characters are often quite reasonable despite lateral transfers of genetic material between taxa. In the presence of lateral transfers, outer planar networks furnish a better description of evolution than phylogenetic trees. We present a polynomial-time reconstruction algorithm for perfect outer planar networks with a fixed number of states, characters, and lateral transfers.

Phylogenetic Tools in Astrophysics

“…These distances are computed from the characters and the algorithms are generally extremely fast and efficient. It has always been somewhat surprising that character-and distance-based approaches yield similar results since the mathematical connection is still not obvious [9,10] . This might be due at least partly to the fact that the characters have an evolutionary information (the phylogenetic signal) that is not entirely lost when computing distances.…”