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Review
. 2014 May 1;6(5):a016147.
doi: 10.1101/cshperspect.a016147.

The Eukaryotic Tree of Life From a Global Phylogenomic Perspective

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Free PMC article
Review

The Eukaryotic Tree of Life From a Global Phylogenomic Perspective

Fabien Burki. Cold Spring Harb Perspect Biol. .
Free PMC article

Abstract

Molecular phylogenetics has revolutionized our knowledge of the eukaryotic tree of life. With the advent of genomics, a new discipline of phylogenetics has emerged: phylogenomics. This method uses large alignments of tens to hundreds of genes to reconstruct evolutionary histories. This approach has led to the resolution of ancient and contentious relationships, notably between the building blocks of the tree (the supergroups), and allowed to place in the tree enigmatic yet important protist lineages for understanding eukaryote evolution. Here, I discuss the pros and cons of phylogenomics and review the eukaryotic supergroups in light of earlier work that laid the foundation for the current view of the tree, including the position of the root. I conclude by presenting a picture of eukaryote evolution, summarizing the most recent progress in assembling the global tree.

Figures

Figure 1.
Figure 1.
Global tree of eukaryotes from a consensus of phylogenetic evidence (in particular, phylogenomics), rare genomic signatures, and morphological characteristics. Numerous eukaryotic groups are shown (not exhaustively), regardless of their taxonomic rank. Cartoons illustrate the diversity constituting the largest assemblages (colored boxes). The branching pattern does not necessarily represent the inferred relationships between the lineages. Dotted lines denote uncertain relationships, including conflicting positions. Note the solid branch leading to haptophytes and rappemonads: This illustrates the strong support for placing haptophytes as sister to SAR(stramenopiles, alveolates, and Rhizaria) in a recent study (Burki et al. 2012b), but this lineage is not included in a colored assemblage because confirmation is needed. The arrows point to possible positions for the eukaryotic root; the solid arrow corresponds to the most popular hypothesis (Amorphea-bikont rooting), the broken arrows represent the alternative hypotheses discussed in the text. (This figure was inspired by a template provided by Y. Eglit.)

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