Phylogenomics and the Tree Of Life

David Posada

University of Vigo, Spain. 

Understanding how the genomes of all living organisms came to be is one of the fundamental challenges in biology and indeed one of Darwin’s dreams. The use of complete genome sequences to reconstruct the evolutionary history of organisms, or phylogenomics, should prove very useful to solve not only the tree of life, but also to answer many important questions about development, metabolism, pathogenicity, physiology or behavior. Indeed, recent studies have revealed the power of the phylogenomic approach, but also its challenges, in particular the presence of inconsistent or incongruent signals from the data, and the large computational burden associated. Although the availability of new genomes should in theory increase resolution, more data is not a panacea, and systematic error from model misspecification may lead phylogenomics methods to converge on the incorrect tree with strong apparent statistical support. Here I will review different phylogenomics approaches, highlighting their advantages and disadvantages, and some of the fundamental problems that will need to be addressed in the near future, like the use of appropriate models of genome evolution that, among other things, tackle the gene tree/species tree problem.

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