Mitochondrial Genomics of Ostariophysan Fishes: Perspectives on Phylogeny and Biogeography Kenji Saitoh, 1 Masaki Miya, 2 Jun G. Inoue, 3 Naoya B. Ishiguro, 3 Mutsumi Nishida 3 1 Tohoku National Fisheries Research Institute, Shinhama, Shiogama 985-0001, Japan 2 Natural History Museum and Institute, Chiba, Chuo, Chiba 260-8682, Japan 3 Ocean Research Institute, University of Tokyo, Nakano, Tokyo 164-8639, Japan Received: 27 May 2002 /Accepted: 28 November 2002 Abstract. Ostariophysi is the second largest super- order within Teleostei. It contains five orders: Gon- orynchiformes, Cypriniformes, Characiformes, Siluriformes, and Gymnotiformes. Resolving the higher-level relationships among ostariophysan and related fishes will aid in resolving basal teleostean divergence and provide basis to historical biogeo- graphic analysis of major freshwater fish groups. In thisstudy,wereportthecompletemitochondrial(mt) DNA sequences for eleven ostariophysan fishes and the results of phylogenetic analyses including these species plus four other ostariophysan and nine non- ostariophysanteleosteanfishes.Maximumlikelihood and maximum parsimony analyses reconfirmed clu- peiforms as the closest relatives of ostariophysans. However, gonorynchiforms were closer to clupei- forms than to otophysans (ostariophysan groups ex- cluding gonorynchiforms), thus raising a question over the current definition of Ostariophysi. The lack of clarity in otocephalan (ostariophysans + clupei- forms) basal relationships implies that such diver- gence took place over a short period of time. The monophyly of cypriniforms, characiphysans (char- aciforms,siluriforms,andgymnotiforms),andorders or superorders outside the ostariophysans examined here were conceivably reconstructed. The phyloge- netic hypothesis suggests a Pangean origin of oto- physans. Within characiphysans, gymnotiforms and siluriforms have independent evolutionary origins and evolutionary histories comparable to or older than that of characiforms. This helps to explain the present geographic distribution of characiphysans. Key words: Teleost phylogeny — Regional boot- strap — Zoogeography — Freshwaterfishdiversity Introduction Teleostean fishes include about 23,500 species, amounting to nearly half of the extant vertebrate species(Nelson1994).WithinTeleostei,Ostariophysi is the second largest superorder, with five orders containing63families,nearly1000genera,andabout 6500 species (Nelson 1994; Berra 2001). Except for Gonorynchiformes (e.g., milkfish), all the ostario- physan fishes (Cypriniformes, carps and loaches; Characiformes, tetras; Siluriformes, catfishes; Gym- notiformes, electric eels) have a specialized bony connection of transformed anterior vertebrae be- tween the inner ear and swim-bladder. While gono- rynchiforms (Anotophysi) live in mostly estuarine or marineenvironments,thebonyswim-bladderedfishes (Otophysi) are almost exclusively primary freshwater inhabitants, which occur in all continents except Australia (Fig. 1). About 93% of primary freshwater fish species are Ostariophysi (Berra 2001). Because the volume of freshwater rivers and lakes worldwide collectivelyamounttolessthan 1 2600 ofthatofoceanic J Mol Evol (2003) 1 56:464–472 DOI: 10.1007/s00239-002-2417-y Correspondence to: K. Saitoh; email: ksaitoh@affrc.go.jp