Mitochondrial genome structure and evolution in the living fossil vampire squid, Vampyroteuthis infernalis, and extant cephalopods Shin-ichi Yokobori a, * , Dhugal J. Lindsay b , Mari Yoshida a , Kotaro Tsuchiya c , Akihiko Yamagishi a , Tadashi Maruyama b , Tairo Oshima a,1 a Laboratory of Cellular Biochemistry, Department of Molecular Biology, School of Life Science, Tokyo University of Pharmacy and Life Sciences, 1432-1 Horinouchi, Hachioji, Tokyo 192-0392, Japan b Research Program for Marine Biology and Ecology, Extremobiosphere Research Center, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Kanagawa 237-0061, Japan c Department of Ocean Sciences, Faculty of Marine Science, Tokyo University of Marine Science and Technology, 4-5-7, Konan, Minato-ku, Tokyo 108-8477, Japan Received 25 September 2006; revised 9 May 2007; accepted 13 May 2007 Available online 25 May 2007 Abstract Complete nucleotide sequences of mitochondrial (mt) genomes of the ‘‘living fossil’’ cephalopod Vampyroteuthis infernalis (Vampyr- omorpha) and the cuttlefish Sepia esculenta (Sepiida) were determined. The V. infernalis mt genome structure is identical to the incirrate octopod Octopus vulgaris mt genome structure, and is therefore more similar to that of the polyplacophoran Katharina tunicata, than to that of the other ‘‘living fossil’’ cephalopod Nautilus macromphalus. The mt genome structure of S. esculenta is identical to that of Sepia officinalis. Molecular phylogenetic analyses based on the mt protein genes from the completely sequenced cephalopod mt genomes sug- gested the monophyletic relationship of two myopsid squids Loligo bleekeri and Sepiotheuthis lessoniana, and the monophyletic relation- ship of two oegopsid squids Watasenia scintillans, and Todarodes pacificus. Sepiida appeared as the sister group of Teuthida (Myopsida + Oegopsida). The phylogenetic position of Vampyromorpha appeared as the sister group of Octopoda, although the mono- phyly of Vampyromorpha and Decapodiformes cannot be rejected outright by our phylogenetic analyses. The hypothesis that Vampyr- omorpha is basal among the coleoid cephalopods can be rejected because of low statistical support. Therefore, it is reasonable to recognize three major groups in Coleoidea—Vampyromorpha, Octopoda, and Decapodiformes. Ó 2007 Elsevier Inc. All rights reserved. Keywords: Vampyroteuthis infernalis; Sepia esculenta; Mitochondrial genome; Cephalopod phylogeny 1. Introduction Metazoan mitochondrial (mt) genome sequence infor- mation can be very useful for phylogenetic reconstructions. Most metazoan mt genomes carry the same number and type of genes—two ribosomal RNA genes, 22 transfer RNA genes, and 13 protein genes, with some exceptions (Boore, 1999; but see also Yokobori et al., 2004). In most cases, all corresponding mt genes can be treated as ortholo- gous genes. This is a great advantage for the analysis of mt genes compared to nuclear genes, because these often have many paralogous genes which complicate analysis. In addi- tion, gene organization of metazoan mt genomes, the mt genetic code, and other higher information on mt genomes have been found to be powerful tools for phylogenetic reconstructions (e.g. Boore and Brown, 1998; Boore, 1999). Mollusca is one of the major metazoan phyla. Species can be found in oceans and freshwater as well as terrestrial environments. Cephalopoda is the third most speciose class of Mollusca, with all members marine. Extant cephalopods are subdivided into the Nautiloidea (nautiluses) and 1055-7903/$ - see front matter Ó 2007 Elsevier Inc. All rights reserved. doi:10.1016/j.ympev.2007.05.009 * Corresponding author. Fax: +81 (0) 42 676 7145. E-mail address: yokobori@ls.toyaku.ac.jp (S. Yokobori). 1 Present address: Institute of Environmental Microbiology, Kyowa Kako Co., Ltd., Machida, Tokyo 194-0035, Japan. www.elsevier.com/locate/ympev Molecular Phylogenetics and Evolution 44 (2007) 898–910