Phylogenomics and the reconstruction of the tree of life

Key PointsUnderstanding phylogenetic relationships among organisms is a prerequisite of evolutionary studies, as contemporary species all share a common history through their ancestry.The wealth of sequence data generated by large-scale genome projects is transforming phylogenetics — the reconstruction of evolutionary history — into phylogenomics.Traditional sequence-based methods of phylogenetic reconstruction (supermatrix and supertree approaches) can also be used at the genome level.New methods based on whole-genome features are also currently being developed to infer phylogenomic trees.Recent studies have revealed the potential of phylogenomic methods for answering long-standing phylogenetic questions.The supermatrix approach that analyses the concatenation of multiple gene sequences is the best-characterized method. Its potential relies on the increased resolving power provided by the use of a large number of sequence positions, which reduces the sampling error.Including large amounts of data in phylogenomic analyses increases the possibility of obtaining highly supported but incorrect phylogenetic results that are due to inconsistency — that is, the convergence towards an incorrect solution as more data are added.Inconsistency arises because current phylogenetic reconstruction methods do not account for the full complexity of the molecular evolutionary process in their underlying assumptions.The risks of inconsistency in phylogenomics analyses can be reduced by the development of better models of sequence evolution, by the critical evaluation of data properties and by the use of only the most reliable characters.Corroboration of phylogenomic results is an important issue, as whole genomes represent the ultimate source of phylogenetically informative characters. Sources of corroboration include the congruence of results obtained using different phylogenomic methods, and their robustness to taxon sampling.The very nature of the evolutionary process and the limitations of current phylogenetic reconstruction methods imply that parts of the tree of life might prove difficult, if not impossible, to resolve with confidence.