Molecular Phylogenetics and Evolution 41 (2006) 636–662 www.elsevier.com/locate/ympev 1055-7903/$ - see front matter  2006 Elsevier Inc. All rights reserved. doi:10.1016/j.ympev.2006.05.044 A phylogenetic analysis of the major groups of catWshes (Teleostei: Siluriformes) using rag1 and rag2 nuclear gene sequences John P. Sullivan a,¤ , John G. Lundberg a , Michael Hardman b,1 a Department of Ichthyology, Academy of Natural Sciences, 1900 Benjamin Franklin Parkway, Philadelphia, PA 19103, USA b Natural History Museum of Los Angeles County, 900 Exposition Boulevard, Los Angeles, CA 90007, USA Received 18 February 2006; revised 22 May 2006; accepted 23 May 2006 Available online 10 June 2006 Abstract Higher-level relationships among catWshes were investigated by parsimony, maximum likelihood and Bayesian analyses of two nuclear genes across 110 catWsh species representing 36 of 37 families and Conorhynchos (family incertae sedis). Analysis of 3660 aligned base pairs from the rag1 and rag2 genes conWrms monophyly of Siluriformes, of most siluriform families and of a number of multifamily groups, some recognized, some novel. South American Loricarioidei are recovered as the sistergroup to other catWshes which are divided into Diplomystidae and Siluroidei. This result contrasts with the prevailing hypothesis that Diplomystidae is the sister to all other catWshes. Monophyly of Siluroidei is supported by rag data including a unique three-codon deletion from rag1. Deep within Siluroidei are 12 large, strongly supported groups with poorly resolved interrelationships. Five are single families: Cetopsidae, Plotosidae, Chacidae, Siluridae and Pangasiidae. Four others are monophyletic taxa ranked here as superfamilies: Clarioidea (Clariidae, Heteropneustidae), Arioidea (Ariidae, Anchariidae), Pimelodoidea (Pimelodidae, Pseudopimelodidae, Heptapteridae, Conorhynchos), Ictaluroidea (Ictaluri- dae, Cranoglanididae). South American Doradoidea (Doradidae, Auchenipteridae) and Aspredinidae are a sistergroup pair. Sisoroidea (without Aspredinidae), Ailia + Laides, Horabagridae, and Bagridae (without Rita) form a large, predominantly Asian clade, “Big Asia.” Mochokidae, Malapteruridae, Amphiliidae, Claroteidae, and African schilbids are united as a species-rich African clade, “Big Africa.” The three large continental clades, “Big Asia,” “Big Africa” and Neotropical Loricarioidei suggest a prevalence of intracontinental diver- siWcation of catWshes. South America is the home of the Gymnotiformes, putative sistergroup of catWshes, plus two of the deepest siluri- form clades, Loricarioidei and Diplomystidae, thus suggesting an ancient siluriform presence if not origin there. The rag phylogeny does not identify any African-South American catWsh clade. The well-known African-Asian relationships within families Clariidae and Bagri- dae are conWrmed, as is the recently found North American-Asian relationship between Ictaluridae and Cranoglanididae.  2006 Elsevier Inc. All rights reserved. Keywords: Siluriformes; Phylogeny; Systematics; Biogeography 1. Introduction CatWshes (Order Siluriformes) are a wonderfully diverse clade with over 3000 valid living species (C.J. Ferraris Jr., pers. com.; Eschmeyer et al., 2004) plus an estimated 1750 undescribed species (Sabaj et al., 2004). In the Wrst six years of the 21st century 332 new catWsh species were described, and among these are the Wrst representatives of nine new genera and one new family (C.J. Ferraris Jr., pers. com.; Eschmeyer, op. cit.). This high rate of discovery shows no sign of diminishing. In no small part this is due to the All CatWsh Species Inventory (ACSI), a multiyear initiative begun in 2003 with funding from the US National Science Foundation’s Planetary Biodiversity Inventories Program (Sabaj et al., 2004). ACSI is leading a global eVort to dis- cover, name and classify all siluriform species. In addition to its central “all species” goal, ACSI is advancing the discovery of the phylogenetic relationships among family-level and higher catWsh groups that are * Corresponding author. E-mail address: sullivan@acnatsci.org (J.P. Sullivan). 1 Present address: METLA, Vantaa Research Center, PL18, 01301, Fin- land. Fax: +1 215 405 5080.