Large scale evaluation of differences between network-based and pairwise sequence-alignment-based methods of dendrogram reconstruction

TL;DR

This study compares network-based and sequence-alignment methods for reconstructing dendrograms, analyzing their differences across various organism sets, and validates a metabolic network approach for broader evolutionary inference.

Contribution

It introduces a systematic comparison of dendrograms from different methodologies and validates a metabolic network-based approach for inferring evolutionary relationships.

Findings

Sequence-alignment and network-based dendrograms differ significantly.

Metabolic network comparison allows for analysis of distantly related organisms.

The systematic approach is validated as effective for evolutionary inference.

Abstract

Dendrograms are a way to represent evolutionary relationships between organisms. Nowadays, these are inferred based on the comparison of genes or protein sequences by taking into account their differences and similarities. The genetic material of choice for the sequence alignments (all the genes or sets of genes) results in distinct inferred dendrograms. In this work, we evaluate differences between dendrograms reconstructed with different methodologies and obtained for different sets of organisms chosen at random from a much larger set. A statistical analysis is performed in order to estimate the fluctuation between the results obtained from the different methodologies. This analysis permit us to validate a systematic approach, based on the comparison of the organisms' metabolic networks for inferring dendrograms. It has the advantage that it allows the comparison of organisms very far away in the evolutionary tree even if they have no known ortholog gene in common.