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MBE Advance Access originally published online on September 26, 2008
Molecular Biology and Evolution 2008 25(12):2689-2698; doi:10.1093/molbev/msn213
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© 2008 The Authors
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

Research Articles

The Apicomplexan Whole-Genome Phylogeny: An Analysis of Incongruence among Gene Trees

Chih-Horng Kuo*,1, John P. Wares* and Jessica C. Kissinger*,{dagger},{ddagger}

* Department of Genetics, University of Georgia
{dagger} Center for Tropical and Emerging Global Diseases, University of Georgia
{ddagger} Institute of Bioinformatics, University of Georgia

E-mail: chkuo{at}email.arizona.edu.

Accepted for publication September 18, 2008.

The protistan phylum Apicomplexa contains many important pathogens and is the subject of intense genome sequencing efforts. Based upon the genome sequences from seven apicomplexan species and a ciliate outgroup, we identified 268 single-copy genes suitable for phylogenetic inference. Both concatenation and consensus approaches inferred the same species tree topology. This topology is consistent with most prior conceptions of apicomplexan evolution based upon ultrastructural and developmental characters, that is, the piroplasm genera Theileria and Babesia form the sister group to the Plasmodium species, the coccidian genera Eimeria and Toxoplasma are monophyletic and are the sister group to the Plasmodium species and piroplasm genera, and Cryptosporidium forms the sister group to the above mentioned with the ciliate Tetrahymena as the outgroup. The level of incongruence among gene trees appears to be high at first glance; only 19% of the genes support the species tree, and a total of 48 different gene-tree topologies are observed. Detailed investigations suggest that the low signal-to-noise ratio in many genes may be the main source of incongruence. The probability of being consistent with the species tree increases as a function of the minimum bootstrap support observed at tree nodes for a given gene tree. Moreover, gene sequences that generate high bootstrap support are robust to the changes in alignment parameters or phylogenetic method used. However, caution should be taken in that some genes can infer a "wrong" tree with strong support because of paralogy, model violations, or other causes. The importance of examining multiple, unlinked genes that possess a strong phylogenetic signal cannot be overstated.

Key Words: Apicomplexa • genome scale • phylogeny • bootstrap • long-branch attraction • taxon sampling

1 Present address: Department of Ecology and Evolutionary Biology, University of Arizona

Hervé Philippe, Associate Editor


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