Phylogenetic relationships within the speciose family Characidae (Teleostei: Ostariophysi: Characiformes) based on multilocus analysis and extensive ingroup sampling

Background: With nearly 1,100 species, the fish family Characidae represents more than half of the species of Characiformes, and is a key component of Neotropical freshwater ecosystems. The composition, phylogeny, and classification of Characidae is currently uncertain, despite significant efforts based on analysis of morphological and molecular data. No consensus about the monophyly of this group or its position within the order Characiformes has been reached, challenged by the fact that many key studies to date have non-overlapping taxonomic representation and focus only on subsets of this diversity. Results: In the present study we propose a new definition of the family Characidae and a hypothesis of relationships for the Characiformes based on phylogenetic analysis of DNA sequences of two mitochondrial and three nuclear genes (4,680 base pairs). The sequences were obtained from 211 samples representing 166 genera distributed among all 18 recognized families in the order Characiformes, all 14 recognized subfamilies in the Characidae, plus 56 of the genera so far considered incertae sedis in the Characidae. The phylogeny obtained is robust, with most lineages significantly supported by posterior probabilities in Bayesian analysis, and high bootstrap values from maximum likelihood and parsimony analyses. Conclusion: A monophyletic assemblage strongly supported in all our phylogenetic analysis is herein defined as the Characidae and includes the characiform species lacking a supraorbital bone and with a derived position of the emergence of the hyoid artery from the anterior ceratohyal. To recognize this and several other monophyletic groups within characiforms we propose changes in the limits of several families to facilitate future studies in the Characiformes and particularly the Characidae. This work presents a new phylogenetic framework for a speciose and morphologically diverse group of freshwater fishes of significant ecological and evolutionary importance across the Neotropics and portions of Africa.

We thank all the individuals and institutions who assisted us in the collection and identification of the specimens that served as the basis for this study, with special thanks to Mauro Nirchio, Universidad de Oriente, for the donation of tissue samples from Venezuela, Oris Sanjur, Smithsonian Tropical Research Institute, for the donation of tissue samples from Panama, Martha Valdez-Moreno, El Colegio de la Frontera Sur, for the donation of tissue samples from Mexico, Hernán Ortega, Museo de Historia Natural, Universidad Nacional Mayor de San Marcos, for the donation of tissue samples from Peru, the American Museum of Natural History for the donation of tissue samples of some Cheirodontinae, and Osvaldo T. Oyakawa, Janice Cunha, Caroline Doria, Riviane Garcez, and Gislene Torrente-Vilara for the donation of tissue samples from several regions within Brazil. We also thank Markus Alexandrou for his help with the Bayesian analyses. The manuscript was substantially improved with the help of the Associated Editor of BMC and three anonymous reviewers. This study is part of the FAPESP (Fundação de Apoio à Pesquisa do Estado de São Paulo) Thematic Project "Phylogenetic relationships in the Characidae (Ostariophysi: Characiformes) (FAPESP grant number 04/09219-6, R.M.C. Castro, Principal Investigator). The first and eighth authors are CNPq (Conselho Nacional de Desenvolvimento Científico e Tecnológico do Brasil) researchers (CNPq grants numbers 309632/2007-2, 303854/2009-0, respectively). The second, third, fourth and fifth authors were supported by FAPESP (06/05744-4, 06/06749-0, 06/04551-8, 06/00545-3, respectively). A Research Coordination Network (RCN) grant from the U.S. National Science Foundation (DEB-0443470, PI = G. Ortí) provided funding for a student exchange program supporting the fourth author.