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  • Review Article
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Phylogenomics and the reconstruction of the tree of life

Nature Reviews Genetics volume 6, pages 361–375 (2005)Cite this article

Key Points

  • Understanding 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.

Abstract

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.

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Figure 1: Phylogenomics and the tree of life.
Figure 2: 'Garbage in, garbage out': inconsistency and the use of reliable characters.
Figure 3: Phylogenomics and the resolution of phylogenetic trees.

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Acknowledgements

We thank N. Rodrigue, N. Rodríguez-Ezpeleta and E. Douzery for critical reading of early versions of the manuscript. Constructive comments from three anonymous referees also helped to make the manuscript more accurate. We apologize to our colleagues whose relevant work has not been cited because of space limitations. The authors gratefully acknowledge the financial support provided by Génome Québec, Canada, the Canadian Research Chair and the Université de Montréal, Canada.

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  1. Département de Biochimie, Canadian Institute for Advanced Research, Centre Robert-Cedergren, Université de Montréal, Succursale Centre-Ville, Montréal, Québec, H3C3J7, Canada

    Frédéric Delsuc, Henner Brinkmann & Hervé Philippe

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  1. Frédéric Delsuc
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Correspondence to Hervé Philippe.

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FURTHER INFORMATION

Assembling the Fungal Tree of Life

Assembling the Tree of Eukaryotic Diversity — Eu-Tree

Assembling the Tree of Life — Diptera

Assembling the Tree of Life — Early Bird

Biodic web site

Blaxter Laboratory Nematode Genomics web site

Cyberinfrastructure for Phylogenetic Research (CIPRes) Project

DeepTime Project

EBI ClustalW Program

EMBL Nucleotide Sequence Database

Gblocks web site

GOLD Genomes OnLine Database

Green Plant Phylogeny Research Coordination Group — DeepGreen

Higher-Level Arthropod Phylogenomics from the Cunnigham Laboratory

NCBI BLAST

NCBI — National Center for Biotechnology Information

Nematode Genome Sequencing Center

PAUP*

PhyCom — a Phylogenetic Community

Phylogeny Programs at Joe Felsenstein's web page

PHYML

Protist EST Program (PEP)

TreeBASE

Tree of Life Web Project

Glossary

HOMOLOGOUS CHARACTERS

Homologous characters are those that are descended from a common ancestor.

PRIOR PROBABILITY

The probability of a hypothesis (or parameter value) without reference to the available data. This can be derived from first principles, or based on general knowledge or previous experiments.

NODE

Nodes of phylogenetic trees represent taxonomic units. Internal nodes (or branches) refer to hypothetical ancestors, whereas terminal nodes (or leaves) generally correspond to extant species.

INCONSISTENCY

A phylogenetic reconstruction method is statistically inconsistent if it converges towards supporting an incorrect solution with increasing confidence as more data is analysed.

HOMOPLASY

Identical character states (for example, the same nucleotide base in a DNA sequence) that are not the result of common ancestry (not homologous), but that arose independently in different ancestors by convergent mutations.

CONVERGENCE

The independent evolution of similar character states in evolutionarily distinct lineages.

REVERSAL

The independent reacquisition of the ancestral character state in a given evolutionary lineage.

HOMOLOGY

Two sequences are homologous if they share a common ancestor.

ORTHOLOGY

Two sequences are orthologous if they share a common ancestor and originated by speciation.

HEURISTIC

A method of inference that relies on educated guesses or simplifications that limit the parameter space over which solutions are searched. This approach is not guaranteed to find the correct answer.

BREAKPOINT

In the context of phylogenetic methods that are based on gene-order comparison between genomes, a breakpoint is defined when a pair of genes are adjacent in one genome but not in the other.

HORIZONTAL GENE TRANSFER

The transfer of genetic material between the genomes of two organisms, which usually belong to different species, that does not occur through parent–progeny routes.

PARALLEL GENE LOSS

The independent loss of homologous genes in evolutionary distinct lineages.

SATURATION

Mutational saturation occurs when many changes at a given position have randomized the genuine phylogenetic signal.

ROOT

The root of a phylogenetic tree represents the common ancestor of all taxa that are represented in the tree. The position of the root is often determined using an outgroup taxon to determine the order of evolution in the group of taxa of interest.

MONOPHYLY

Monophyletic taxa include all the species that are derived from a single common ancestor.

STOCHASTIC OR SAMPLING ERROR

The error in phylogenetic estimates caused by the finite length of the sequences used in the inference. As the size of the sequences increases, the magnitude of the stochastic error decreases.

SYSTEMATIC ERROR

The error in phylogenetic estimates that is due to the failure of the reconstruction method to fully account for the properties of the data.

BOOTSTRAP ANALYSIS

A type of statistical analysis used to test the reliability of specific branches in an evolutionary tree. The non-parametric bootstrap proceeds by re-sampling the original data, with replacement, to create a series of bootstrap samples of the same size as the original data. The bootstrap percentage of a node is the proportion of times that node is present in the set of trees that is constructed from the new data sets.

BAYESIAN POSTERIOR PROBABILITY

In Bayesian phylogenetics, the posterior probability of a particular node of a tree is the probability that the node is correct, which is conditional on the data and the model used in the analysis both being correct.

HETEROTACHY

The variation of evolutionary rate of a given position of a molecule through time.

MARKOV CHAIN MONTE CARLO

A computational technique for the efficient numerical calculation of likelihoods.

DISK-COVERING METHODS

A family of 'divide-and-conquer' algorithmic methods for large-scale tree reconstruction. They use graph theory to optimally partition the input dataset into small overlapping sets of closely related species, reconstruct phylogenetic trees from these subsets, and combine the subtrees into one tree for the entire set of species.

COVARION MODEL OF MOLECULAR EVOLUTION

In this model, although some sites in a macromolecule are vital to function and can never change through time, most switch between being free to evolve in some species and being invariable in others.

METAGENOMICS

The functional and sequence-based analysis of the collective microbial genomes contained in an environmental sample of uncultured organisms.

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Delsuc, F., Brinkmann, H. & Philippe, H. Phylogenomics and the reconstruction of the tree of life. Nat Rev Genet 6, 361–375 (2005). https://doi.org/10.1038/nrg1603

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