title: A time-calibrated, multi-locus phylogeny of piranhas and pacus (Characiformes: Serrasalmidae) and a comparison of species tree methods.
abstract: The phylogeny of piranhas, pacus, and relatives (family Serrasalmidae) was inferred on the basis of DNA sequences from eleven gene fragments that include the mitochondrial control region plus 10 nuclear genes (two exons and eight introns). The new data were obtained for a representative sampling of 53 specimens, collected from all major South American rivers, accounting for over 40% of the valid species and all genera excluding Utiaritichthys. Two fossil calibration points and relaxed-clock Bayesian analyses were used to estimate the timing of diversification. The new multilocus dataset also is used to compare several species-tree approaches against the results obtained using the concatenated alignment analyzed under maximum likelihood and Bayesian inference. Individual gene trees showed substantial topological discordance, but analyses based on concatenation and Bayesian and maximum likelihood-based species trees approaches converged onto a single phylogeny. The resulting phylogenetic hypothesis is robust and supports a division of the family into three major clades, consistent with previous results based on mitochondrial DNA alone. The earliest branching event separated a "pacu" clade (Colossoma, Mylossoma and Piaractus) from the rest of the family in the Late Cretaceous (over 68 Ma). The other two clades, that contain most of the diversity, are formed by the "true piranhas" (Metynnis, Pygopristis, Pygocentrus, Pristobrycon, Catoprion, and Serrasalmus) and the Myleus-like pacus (the Myleus clade). The "true" piranha clade originated during the Eocene (∼53 Ma) but the most recent diversification of flesh-eating piranhas within the genera Serrasalmus and Pygocentrus did not start until the Miocene (∼17 Ma). A comparison of species tree approaches indicates that most methods tested are consistent with results obtained by concatenation, suggesting that the gene-tree incongruence observed is mild and will not produce misleading results under simple concatenation analysis. Non-monophyly of several genera (Pristobrycon, Tometes, Myloplus, Mylesinus) and putative species (Serrasalmus rhombeus) was obtained, suggesting that further study of this family is necessary.
authors.affiliation: Department of Biological Sciences, The George Washington University, 2023 G St. NW, Washington, DC 20052, USA.
authors.forename: Andrew W
authors.initials: AW
authors.lastname: Thompson
authors.affiliation: Department of Biological Sciences, The George Washington University, 2023 G St. NW, Washington, DC 20052, USA; Department of Biology, University of Puerto Rico - Rio Piedras, P.O. Box 23360, San Juan, PR 00931, USA.
authors.forename: Ricardo
authors.initials: R
authors.lastname: Betancur-R
authors.affiliation: Department of Natural History, The Royal Ontario Museum, 100 Queens Park, Toronto, ON M5S 2C6, Canada; Department of Ecology and Evolutionary Biology, University of Toronto, 25 Willcocks Street, Toronto, ON M5S 3B2, Canada.
authors.forename: Hernán
authors.initials: H
authors.lastname: López-Fernández
authors.affiliation: Department of Biological Sciences, The George Washington University, 2023 G St. NW, Washington, DC 20052, USA. Electronic address: gorti@gwu.edu.
authors.forename: Guillermo
authors.initials: G
authors.lastname: Ortí
mesh_terms: D000818:Animals; D001499:Bayes Theorem; D005075:Biological Evolution; D002467:Cell Nucleus / Q000235:genetics; D060125:Characiformes / Q000145:classification* / Q000235:genetics; D004272:DNA, Mitochondrial / Q000235:genetics; D005580:Fossils; D007438:Introns; D016013:Likelihood Functions; D008957:Models, Genetic; D010802:Phylogeny; D017422:Sequence Analysis, DNA
chemical_list: D004272:DNA, Mitochondrial
keywords: Fossil calibration; Mitochondrial DNA; Nuclear introns; Species trees