Phylogenomics and the reconstruction of the tree of life

REVIEWSPHYLOGENOMICS AND THE

RECONSTRUCTION OF

THE TREE OF LIFEFrdric Delsuc, Henner Brinkmann and Herv PhilippeAbstract | As more complete genomes are sequenced, phylogenetic analysis is entering a new

era that of phylogenomics. One branch of this expanding field aims to reconstruct the

evolutionary history of organisms on the basis of the analysis of their genomes. Recent studies

have demonstrated the power of this approach, which has the potential to provide answers to

several fundamental evolutionary questions. However, challenges for the future have also been

revealed. The very nature of the evolutionary history of organisms and the limitations of current

phylogenetic reconstruction methods mean that part of the tree of life might prove difficult, if not

impossible, to resolve with confidence.Understanding phylogenetic relationships between

organisms is a prerequisite of almost any evolutionary

study, as contemporary species all share a common history through their ancestry. The idea of phylogeny follows directly from the theory of evolution presented by

Charles Darwin in The Origin of Species1: the only illustration in his famous book is the first representation of

evolutionary relationships among species, in the form

of a phylogenetic tree. The subsequent enthusiasm of

biologists for the phylogenetic concept is illustrated by

the publication of Ernst Haeckels famous trees as early

as 1866 (REF. 2).Today, phylogenetics the reconstruction of evolutionary history relies on using mathematical methods to infer the past from features of contemporary

species, with only the fossil record to provide a window

to the evolutionary history of life on our planet. This

reconstruction involves the identification of HOMOLOGOUSCHARACTERS that are shared between different organisms,

and the inference of phylogenetic trees from the comparison of these characters using reconstruction methods (BOX 1). The accuracy of the inference is therefore

heavily dependent on the quality of models for the

evolution of such characters. Because the underlying

mechanisms are not yet well understood, reconstructing

the evolutionary history of life on Earth solely on the

basis of the information provided by living organisms

has turned out to be difficult.Until the 1970s, which brought the dawn of molecular techniques for sequencing proteins and DNA,

phylogenetic reconstruction was essentially based on

the analysis of morphological or ultrastructural characters. The comparative anatomy of fossils and extant

species has proved powerful in some respects; for