Complete mitochondrial DNA sequence of the endangered frog Odorrana ishikawae (family Ranidae) and unexpected diversity of mt gene arrangements in ranids Atsushi Kurabayashi a , Natsuhiko Yoshikawa a,1 , Naoki Sato a , Yoko Hayashi b,2 , Shohei Oumi c , Tamotsu Fujii b , Masayuki Sumida a, * a Institute for Amphibian Biology, Graduate School of Science, Hiroshima University, Hiroshima 739-8526, Japan b Department of Health Science, Hiroshima Prefectural University, Hiroshima 734-8558, Japan c Section of Agriculture and Forest, Amami City Government, Amami, Kagoshima 894-0048, Japan article info Article history: Received 20 July 2009 Revised 21 December 2009 Accepted 20 January 2010 Available online 25 January 2010 Keywords: Mitochondrial genome Gene rearrangement Ranidae Odorrana abstract We determined the complete nucleotide sequence of the mitochondrial (mt) genome of an endangered Japanese frog, Odorrana ishikawae (family Ranidae). We also sequenced partial mt genomes of three other Odorrana and six ranid species to survey the diversity of genomic organizations and elucidate the phylo- genetic problems remaining in this frog family. The O. ishikawae mt genome contained the 37 mt genes and single control region (CR) typically found in vertebrate mtDNAs, but the region of Light-strand rep- lication origin (OL) was triplicated in this species. Four protein-encoding genes (atp6, nd2, nd3, and nd5) were found to have high sequence divergence and to be usable for population genetics studies on this endangered species. Among the surveyed ranids, only two species (Rana and Lithobates) manifested the typical neobatrachian-type mt gene arrangement. In contrast, relatively large gene rearrangements were found in Amolops, Babina, and Staurois species; and translocations of single tRNA genes (trns) were observed in Glandirana and Odorrana species. Though the inter-generic and interspecific relationships of ranid taxa remain to be elucidated based on 12S and 16S rrn sequence data, some of the derived mt gene orders were found to have synapomorphic features useful for solving problematic ranid phylogenies. The tandem duplication and random loss (TDRL) model, the traditional model for mt gene rearrangement, failed to easily explain several of the mt gene rearrangements observed here. Indeed, the recent recom- bination-based gene rearrangement models seemed to be more suitable for this purpose. The high fre- quency of gene translocations involving a specific trn block (trnH-trnS1) and several single tRNA genes suggest that there may be a retrotranslocation in ranid mt genomes. Ó 2010 Elsevier Inc. All rights reserved. 1. Introduction Odorrana ishikawae is an anuran species endemic to only two small Japanese Islands, Okinawa and Amami. By some descrip- tions, the species is the most beautiful frog in this country. Yet sadly, over-hunting and environmental destruction have recently devastated the populations of this species. O. ishikawae has been listed as a class B1 endangered species in IUCN Red List of Threatened Species (http://www.iucnredlist.org), and designated as a natural monument in both Okinawa and Kagoshima Prefec- tures. Prompt measures to conserve this species are awaited, but usable information on the interpopulation genetic divergence is not yet available. The taxonomic history of Odorrana ishikawae is somewhat com- plicated. Initially, this frog was described as a rhacophorid species (Buergeria ishikawae; Stejneger, 1901). Then it was moved to sev- eral ranid genera (i.e., Rana and Huia), and most recently it has been classified as Odorrana (Cai et al., 2007; Frost, 2009). Many other species now recognized as Odorrana had also been formerly classified as members of other ranid genera (e.g., Amolops, Hylarana, Huia, and Rana; see Frost, 2009), and the taxonomic affil- iations related to this genus can still be confounding (Cai et al., 2007; Che et al., 2007; Stuart, 2008). The generic affiliations between Odorrana and Amolops species have been especially problematic. O. tormota, a species famous for its ultrasonic- communication, serves as a good example. This frog was regarded as a member of Amolops in earlier decades, and is still often de- scribed by the synonym ‘‘A. tormotus.” Furthermore, no consensus has been reached on the interspecific relationships within the 1055-7903/$ - see front matter Ó 2010 Elsevier Inc. All rights reserved. doi:10.1016/j.ympev.2010.01.022 * Corresponding author. Fax: +81 82 424 0739. E-mail address: msumida@hiroshima-u.a.c.jp (M. Sumida). 1 Present address: Graduate School of Human and Environmental Studies, Kyoto University, Kyoto 606-8501, Japan. 2 Present address: Natural Science Center for Basic Research and Development (N- BARD), Hiroshima University, Hiroshima 734-8551, Japan. Molecular Phylogenetics and Evolution 56 (2010) 543–553 Contents lists available at ScienceDirect Molecular Phylogenetics and Evolution journal homepage: www.elsevier.com/locate/ympev