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A time-calibrated, multi-locus phylogeny of piranhas and pacus (Characiformes: Serrasalmidae) and a comparison of species tree methods

Thompson, Andrew W., Betancur-R., Ricardo, López-Fernández, Hernán, Ortí, Guillermo
Molecular phylogenetics and evolution 2014 v.81 pp. 242-257
Serrasalmus rhombeus, rivers, Metynnis, mitochondrial DNA, fossils, Mylossoma, Colossoma, Piaractus mesopotamicus, branching, Bayesian theory, data collection, phylogeny, Myleus, mitochondria, topology, exons, Pygocentrus, introns
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 68Ma). 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 (∼53Ma) but the most recent diversification of flesh-eating piranhas within the genera Serrasalmus and Pygocentrus did not start until the Miocene (∼17Ma). 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.