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Published online on June 19, 2006, 10.1073/pnas.0603797103 OPEN ACCESS ARTICLE


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Evolution
Pegasoferae, an unexpected mammalian clade revealed by tracking ancient retroposon insertions

( intron | long interspersed element 1 | mammalian phylogeny )

Hidenori Nishihara {dagger}, Masami Hasegawa {ddagger}{sect}, and Norihiro Okada {dagger}¶||

{dagger}Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, Yokohama 226-8501, Japan; {ddagger}Department of Statistical Modeling, Institute of Statistical Mathematics, Tokyo 106-8569, Japan; {sect}Department of Biosystems Science, Graduate University for Advanced Studies, Hayama, Kanagawa 240-0193, Japan; and Division of Speciation, National Institute of Basic Biology, Okazaki 444-8585, Japan

Communicated by Margaret G. Kidwell, University of Arizona, Tucson, AZ, May 9, 2006 (received for review January 25, 2006)

Despite the recent large-scale efforts dedicated to comprehensive phylogenetic analyses using mitochondrial and nuclear DNA sequences, several relationships among mammalian orders remain controversial. Here, we present an extensive application of retroposon (L1) insertion analysis to the phylogenetic relationships among almost all mammalian orders. In addition to demonstrating the validity of Glires, Euarchontoglires, Laurasiatheria, and Boreoeutheria, we demonstrate an interordinal clade that links Chiroptera, Carnivora, and Perissodactyla within Laurasiatheria. Re-examination of a large DNA sequence data set yielded results consistent with our conclusion. We propose a superordinal name "Pegasoferae" for this clade of Chiroptera + Perissodactyla + Carnivora + Pholidota. The presence of a single incongruent L1 locus generates a tree in which the group of Carnivora + Perissodactyla associates with Cetartiodactyla but not with Chiroptera. This result suggests that incomplete lineage sorting of an ancestral dimorphism occurred with regard to the presence or absence of retroposon alleles in a common ancestor of Scrotifera (Pegasoferae + Cetartiodactyla), which was followed by rapid divergence into the extant orders over an evolutionarily short period. Accordingly, Euungulata (Cetartiodactyla + Perissodactyla) and Fereuungulata (Carnivora + Pholidota + Perissodactyla + Cetartiodactyla) cannot be validated as natural groups. The interordinal mammalian relationships presented here provide a cornerstone for future studies in the reconstruction of mammalian classifications, including extinct species, on evolution of large genomic sequences and structure, and in developmental analysis of morphological diversification.

Author contributions: H.N. and N.O. designed research; H.N. performed research; M.H. analyzed data; and H.N., M.H., and N.O. wrote the paper.

Conflict of interest statement: No conflicts declared.

Freely available online through the PNAS open access option.

||To whom correspondence should be addressed.

Norihiro Okada, E-mail: nokada{at}bio.titech.ac.jp

www.pnas.org/cgi/doi/10.1073/pnas.0603797103
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