Live neighbor-joining

Guilherme P Telles,Nalvo F Almeida,Graziela S Araújo,Maria E M T Walter,Marcelo M Brigido

doi:10.1186/s12859-018-2162-x

Abstract

BackgroundIn phylogenetic reconstruction the result is a tree where all taxa are leaves and internal nodes are hypothetical ancestors. In a live phylogeny, both ancestral and living taxa may coexist, leading to a tree where internal nodes may be living taxa. The well-known Neighbor-Joining heuristic is largely used for phylogenetic reconstruction.ResultsWe present Live Neighbor-Joining, a heuristic for building a live phylogeny. We have investigated Live Neighbor-Joining on datasets of viral genomes, a plausible scenario for its application, which allowed the construction of alternative hypothesis for the relationships among virus that embrace both ancestral and descending taxa. We also applied Live Neighbor-Joining on a set of bacterial genomes and to sets of images and texts. Non-biological data may be better explored visually when their relationship in terms of content similarity is represented by means of a phylogeny.ConclusionOur experiments have shown interesting alternative phylogenetic hypothesis for RNA virus genomes, bacterial genomes and alternative relationships among images and texts, illustrating a wide range of scenarios where Live Neighbor-Joining may be used.

Highlights

In phylogenetic reconstruction the result is a tree where all taxa are leaves and internal nodes are hypothetical ancestors
We present the application of Live Neighbor-Joining to three different sets of RNA virus genomes: Zika, Chikungunya and Ebola
In this work we presented a new heuristic for the Distance-Based Live Phylogeny Problem

Summary

Introduction

In phylogenetic reconstruction the result is a tree where all taxa are leaves and internal nodes are hypothetical ancestors. Both ancestral and living taxa may coexist, leading to a tree where internal nodes may be living taxa. The well-known Neighbor-Joining heuristic is largely used for phylogenetic reconstruction. Neighbor-Joining [1] is a widely used heuristic for phylogenetic reconstruction from a distance matrix. In a live phylogeny [3] we admit that both ancestral and current taxa coexist. This is likely to happen for instance with viruses, that evolve at high rates [4,5,6,7]. We must resort to heuristics for obtaining solutions that are as good as possible within reasonable amounts of time and computer resources

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Conclusion