The tree of eukaryotes

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Recent advances in resolving the tree of eukaryotes are converging on a model composed of a few large hypothetical ‘supergroups’, each comprising a diversity of primarily microbial eukaryotes (protists, or protozoa and algae). The process of resolving the tree involves the synthesis of many kinds of data, including single-gene trees, multigene analyses, and other kinds of molecular and structural characters. Here, we review the recent progress in assembling the tree of eukaryotes, describing the major evidence for each supergroup, and where gaps in our knowledge remain. We also consider other factors emerging from phylogenetic analyses and comparative genomics, in particular lateral gene transfer, and whether such factors confound our understanding of the eukaryotic tree.

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Why search for the tree of life?

A well resolved phylogenetic tree, correctly describing the relationships among organisms, is an important tool that is used in many ways, often subconsciously. In the broadest sense, the tree is a means to harness biological information for interpretation or prediction. Processes of change and adaptation can only be understood in the context of a tree because the actions of these processes over time are lost to us without some way of reconstructing long-dead intermediate forms. Reconstructing

The tree of eukaryotes

For eukaryotes, relatively detailed schemes of evolutionary relationships have long been inferred using morphology and biochemistry. Even for microbial eukaryotes, this approach was successful in dividing diversity into a large number of distinct lineages that are still recognized in light of much molecular data. However, it was less successful in determining how these lineages are related to one another, because there are few shared derived characters to unite eukaryotic groups at this level

Dissenting evidence

We have presented a hypothesis for a global phylogeny of eukaryotes where eukaryotic diversity is sequestered into five large groups. Several forms of consistent evidence support each of these groups but, not surprisingly, there are dissenting observations. Even some of the best-supported groups, for example opisthokonts, have been questioned in recent analyses [46]. Indeed, every major lineage of eukaryotes is contradicted by at least one molecular phylogeny, but this does not mean that they

Lateral gene transfer and the tree of eukaryotes

Lateral, or horizontal, gene transfer (LGT) is the movement of genetic information between two distantly related genomes (i.e. not sexual recombination within one species), resulting in a genome that contains an expressed, functional gene from a foreign source. Determining the scale of LGT is important for interpreting molecular phylogenies and the distribution of molecular characteristics in any group. The debate over the impact of LGT on prokaryote evolution has a long history, and this

The future of the tree of eukaryotes

Comparative genomics will have a dramatic and positive effect on our understanding of the tree itself, for two reasons. First, large-scale concatenated data sets covering a broad variety of eukaryotes require more data than are realistically generated by a targeted gene-by-gene approach, but such data will emerge from whole-genome and EST sequencing projects. Second, non-tree-based characters (such as gene fusions, insertions and gene replacements) typically are not intentionally sought, but

Acknowledgements

The authors are members of the Protist EST Program (PEP), supported by funding from Genome Canada, Génome Québec, Genome Atlantic and the Atlantic Canada Opportunities Agency (Atlantic Innovation Fund).

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