Phylogenomics and the reconstruction of the tree of life

Abstract

Correspondence to H.P. email: herve.philippe@umontreal.ca -2 - PrefaceAs 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 based on the analysis of their genomes. Recent studies have demonstrated the power of this approach, which has the potential to provide answers to a number of 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 may prove difficult, if not impossible, to resolve with confidence. Introductory paragraphUnderstanding phylogenetic relationships between organisms is a prerequisite of almost any evolutionary study, as contemporary species all share a common history through their ancestry. The notion of phylogeny follows directly from the theory of evolution presented by Charles Darwin in "The Origin of Species" 1 : 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 Haeckel's famous "trees" as early as 1866 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 on the evolutionary past of life on our planet. This reconstruction involves the identification of HOMOLOGOUS CHARACTERS that are shared among different organisms, and the inference of phylogenetic trees from the comparison of these characters using reconstruction methods (BOX 1). The accuracy of -3 -the inference is therefore heavily dependent upon 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 based solely on 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 example, the main groups of animals and plants have been delineated fairly easily using these methods. However, this approach is hampered by the limited number of reliable homologous characters available; these are almost non-existent in micro-organisms 3 and are rare even in complex organisms.The introduction of the use of molecular data in phylogenetics 4 led to a revolution.In the late 1980s, access to DNA sequences increased the number of homologous characters that could be compared from less than 100 to more than 1,000, ...

Additional molecular support for the new chordate phylogeny

“…The most recent advances in animal phylogeny have come from phylogenomics (Delsuc et al, 2005), which considerably increases the resolving power by considering numerous concatenated genes from expressed sequence tags (ESTs) and complete genome projects (Philippe and Telford, 2006). Despite some troubled beginnings due to the shortcomings of using only a restricted set of taxa (Philippe et al, 2005a), phylogenomics has provided strong corroborating support for the new animal phylogeny, essentially confirming the monophyly of Protostomia, Ecdysozoa, and Lophotrochozoa (Baurain et al, 2007;Dunn et al, 2008;Lartillot and Philippe, 2008;Philippe et al, 2005b).…”

Efficient FPT Algorithms for (Strict) Compatibility of Unrooted Phylogenetic Trees

“…Even though this is, from a theoretical point of view, a big step further toward solving this problem in reasonable time, our running times are still prohibitive to be of any use in real-life phylogenomic studies, where k can go up very quickly [8]. One possibility to design a practical algorithm is to devise reduction rules to keep k small.…”

Chordate origins and evolution

“…Fortunately, the exponential accumulation of molecular data from genomes and animal models comes to the rescue. Molecular phylogenies are continually being constructed, recently incorporating multiple genes on a genomic scale, hopefully reducing sources of systematical errors (Bourlat, 2006;Delsuc et al, 2005;Dunn et al, 2008). The interested developmental biologist is also compelled to understand how fossils can and do change our views on the evolution of development (Conway-Morris, 1994;Hall, 2002).…”