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MBE Advance Access published online on October 28, 2009
Molecular Biology and Evolution, doi:10.1093/molbev/msp263
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© The Author 2009. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. All rights reserved. For permissions, please e-mail: journals.permissions@oxfordjournals.org

Research Article

Large-scale parsimony analysis of metazoan indels in protein-coding genes

Frida Belinky*, Ofir Cohen{dagger} and Dorothée Huchon*

* Department of Zoology, George S. Wise Faculty of Life Sciences, Tel-Aviv University, Tel-Aviv 69978, Israel
{dagger} Department of Cell Research and Immunology, George S. Wise Faculty of Life Sciences, Tel-Aviv University, Tel-Aviv 69978, Israel

Corresponding author: Dorothée Huchon, Department of Zoology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 69978, Israel. Phone: +972 - 3- 6409817. Fax: + 972 - 3- 6409403, E-mail: huchond{at}post.tau.ac.il

Received for publication May 18, 2009. Revision received October 20, 2009. Accepted for publication October 23, 2009.

Insertions and deletions (indels) are considered to be rare evolutionary events, the analysis of which may resolve controversial phylogenetic relationships. Indeed, indel characters are often assumed to be less homoplastic than amino-acid and nucleotide substitutions and, consequently, more reliable markers for phylogenetic reconstruction. In this study we analyzed indels from over a thousand metazoan orthologous genes. We studied the impact of different species sampling, ortholog datasets, lengths of included indels, and indel-coding methods, on the resulting metazoan tree. Our results show that, similar to sequence substitutions, indels are homoplastic characters and their analysis is sensitive to the long-branch attraction artifact. Furthermore, improving the taxon sampling and choosing a closely-related outgroup greatly impact the phylogenetic inference. Our indel-based inferences support the Ecdysozoa hypothesis over the Coelomata hypothesis, and suggest that sponges are a sister clade to other animals.

Key Words: indel • phylogeny • indel coding-method • long-branch attraction • Ecdysozoa • Coelomata


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