The Tree of Life

Abstract

The tree of life, representing the evolution and the relationships between all life-forms, has challenged scientists as soon as Darwin’s work became accepted. A fuel for imagination for a long time, it became more concrete after the molecular biology revolution and the application of mathematical tools to quantify sequence evolution. Despite tremendous advances fueled by the continuous progress in DNA sequencing, from PCR to metagenomics, and in algorithms for phylogenetic reconstruction, many fundamental questions remain still open in the tree of life topology. The biggest of them all would currently be the relationship between Archaea and Eukarya: while some authors argue that they are sister groups (the Woese tree), others state that the latter emerged from the former (the eocyte tree). The tree of life and its subsequent questions are definitely complex objects to comprehend. Evolution states that in order to fully understand life, one has to first know its history, and this mantra should apply here as well. We thus decided to focus in this chapter on the recent history of the tree of life, from its entry into phylogenetics in the 1970s to the recent identification of Asgard archaea and the controversies they have brought. We also briefly discuss the position of the viruses in the tree of life and how their analysis is helpful to understand their host evolution.