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MBE Advance Access published online on December 5, 2005
Molecular Biology and Evolution, doi:10.1093/molbev/msj071
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© The Author 2005. 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
Accepted November 28, 2005

Research Article

Baleen Whale Phylogeny and a Past Extensive Radiation Event Revealed by SINE Insertion Analysis

Masato Nikaido 1, Healy Hamilton 2, Hitomi Makino 1, Takeshi Sasaki 3, Kazuhiko Takahashi 3, Mutsuo Goto 4, Naohisa Kanda 4, Luis A Pastene 4, and Norihiro Okada 5 *

1 Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, Yokohama, Japan
2 California Academy of Sciences, San Francisco, CA
3 Department of Cell Biology, National Institute for Basic Biology, Myodaiji, Okazaki, Japan
4 The Institute of Cetacean Research, Tokyo Japan
5 Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, Yokohama, Japan; Department of Cell Biology, National Institute for Basic Biology, Myodaiji, Okazaki, Japan

* To whom correspondence should be addressed.
Norihiro Okada, E-mail: nokada{at}bio.titech.ac.jp


  Abstract

Baleen whales (suborder Mysticeti) comprise eleven extant species that are classified into four families. Although several phylogenetic hypotheses about these taxa have been proposed, their phylogenetic relationships remain confused. We addressed this problem using SINE (short interspersed repetitive element) insertion data, which now are regarded as almost ideal shared, derived characteristics at the molecular level. We reconstructed the phylogenetic relationships of baleen whales by characterizing 36 informative SINE loci. One of the intriguing conclusions is that balaenopterids and eschrichtiids radiated very rapidly during a very short evolutionary period. During this period, speciation occurred in balaenopterids and eschrichtiids while newly inserted SINE loci remains polymorphic. Later on these SINEs were sorted incompletely into each lineage. Thus, there are now inconsistencies among species regarding the presence or absence of a given SINE. This is in sharp contrast to the phylogeny of toothed whales, for which no SINE inconsistencies have been found. Furthermore, we found monophyletic groupings between humpback and fin whales as well as between (sei + Bryde's) whales and blue whales, both of which have not previously been recognized. The comprehensive SINE insertion data, together with the mitochondrial DNA phylogeny that was recently completed (Sasaki et al., 2005 Syst. Biol. 56:77-90; Rychel, Reeder and Berta 2004, Mol. Phylogenet. Evol. 32:892-901), provide a nearly complete picture of the evolutionary history of baleen whales.

Keywords: baleen whales; phylogeny; radiation event; incomplete lineage sorting.
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