Phylogenetic Relationships Deduced from Whole Genome Comparisons

Abstract

In the second half of the twentieth century, gene sequences have been used to study their evolution as well as the history of species. A decade ago, progress in sequencing techniques provided the opportunity to use whole genome sequences for reconstructing species phylogeny. Several phylogenomic methods have been used to exploit these large amounts of data, and those that are based on homologous or orthologous characters have been favoured. Among these, the supertree and supermatrix approaches have been very successful at resolving parts of the tree of life. However, these methods discard a great proportion of the evolutionary information present in genomes. New integrative models of genome evolution could make a better use of whole genome sequences and thus improve the resolution of the tree of life.

Key concepts

  • Genomes contain a very large amount of information relevant for reconstructing their history and the history of species.

  • Among phylogenomic methods, only those based on homologous/orthologous characters can reconstruct a species tree.

  • Rare genomic changes, supertree and supermatrice methods have been the most extensively used.

  • Genome‐sized datasets have permitted confirming key phylogenies, and have also provided new insights into important parts of the tree of life.

  • New methods that combine different types of genomic information could further improve the resolution of the tree of life.

Keywords: phylogenomics; evolution; gene duplication; lateral gene transfer; trans‐specific polymorphisms

Figure 1.

The many roads to genome trees. Genome trees can be obtained by different types of methods. Two families can be defined: those that need homology/orthology relationships between characters (lower part of the figure), and those that do not (upper part).

Figure 2.

Orthologous characters, and three evolutionary scenarios why character history may differ from the species history. (a) Orthologous characters are characters whose history corresponds to the history of speciations. Here the species tree (large tubular structure) and the gene tree (blue lines) have the same topology, which groups A with B. (b) Duplications (orange circle) and losses complicate the history of characters, and can hide the history of speciations. Here a duplication preceding speciation 1, and character losses after speciation 1 lead to a history different from the species history, where B and C are grouped together, a situation named ‘hidden paralogy’. (c) A lateral transfer from an ancestor of species C to an ancestor of species B also leads to a history where B and C are clustered. (d) Trans‐specific polymorphisms can also render character trees different from the species tree. At any given time in a species, characters can exist in different alleles. At speciation 1, by chance, the ancestors of species B and C possess the blue form of the character, and the ancestor of the species A possesses the red form. The resulting character tree is different from the species tree.

Figure 3.

Integrative models for inferring species phylogeny from whole genomes. All information contained in genomes could be used together, through appropriate models of evolution. Models of sequence evolution allow exploiting events of substitution and possibly events of insertion/deletion, models of gene family evolution events of duplication, loss, transfer and trans‐specific polymorphism, models of character evolution rare genomic changes and models of gene order evolution events of genome rearrangement.

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How to Cite close
Boussau, Bastien(Sep 2009) Phylogenetic Relationships Deduced from Whole Genome Comparisons. In: eLS. John Wiley & Sons Ltd, Chichester. http://www.els.net [doi: 10.1002/9780470015902.a0021784]