Phylogenomics of piranhas and pacus (Serrasalmidae) uncovers how dietary convergence and parallelism obfuscate traditional morphological taxonomy

The Amazon and neighboring South American river basins harbor the world's most diverse assemblages of freshwater fishes. One of the most prominent South American fish families is the Serrasalmidae (pacus and piranhas), found in nearly every continental basin. Serrasalmids are keystone ecological taxa, being some of the top riverine predators as well as the primary seed dispersers in the flooded forest. Despite their widespread occurrence and notable ecologies, serrasalmid evolutionary history and systematics are controversial. For example, the sister taxon to serrasalmids is contentious, the relationships of major clades within the family are inconsistent across different methodologies, and half of the extant serrasalmid genera are suggested to be non-monophyletic. We analyzed exon capture to reexamine the evolutionary relationships among 63 (of 99) species across all 16 serrasalmid genera and their nearest outgroups, including multiple individuals per species to account for cryptic lineages. To reconstruct the timeline of serrasalmid diversification, we time-calibrated this phylogeny using two different fossil-calibration schemes to account for uncertainty in taxonomy with respect to fossil teeth. Finally, we analyzed diet evolution across the family and comment on associated changes in dentition, highlighting the ecomorphological diversity within serrasalmids. We document widespread non-monophyly of genera within Myleinae, as well as between Serrasalmus and Pristobrycon, and propose that reliance on traits like teeth to distinguish among genera is confounded by ecological homoplasy, especially among herbivorous and omnivorous taxa. We clarify the relationships among all serrasalmid genera, propose new subfamily affiliations, and support hemiodontids as the sister taxon to Serrasalmidae.Dryad tree files.zip includes: ASTRAL coalescent tree Nucleotide & amino acid concatenated trees & matrices Scheme 1 & Scheme 2 time-calibrated trees (generated from BEAST2) Funding provided by: National Science FoundationCrossref Funder Registry ID: http://dx.doi.org/10.13039/100000001Award Number: 1712015Funding provided by: National Science FoundationCrossref Funder Registry ID: http://dx.doi.org/10.13039/100000001Award Number: 1541554Funding provided by: National Science FoundationCrossref Funder Registry ID: http://dx.doi.org/10.13039/100000001Award Number: 1929248Funding provided by: National Science FoundationCrossref Funder Registry ID: http://dx.doi.org/10.13039/100000001Award Number: 1932759Funding provided by: Natural Sciences and Engineering Research Council of CanadaCrossref Funder Registry ID: http://dx.doi.org/10.13039/501100000038Award Number: RGOIN-2014-05374Funding provided by: National Science FoundationCrossref Funder Registry ID: http://dx.doi.org/10.13039/100000001Award Number: 1257813These data comprise the Supplemental Files for submission to Systematic Biology S1 - Previous phylogenetic hypotheses for the relationships of Serrasalmidae. S2 - Description of the fossil calibration schemes and rationale for assignment of those fossils to nodes. S3 - References for S2. S4 - Diet classification of extant serrasalmids based on literature review. S5 - References for S4. S6 - Stochastic Character mapping transition matrix for diet states. S7 - Taxonomic recommendations for Serrasalmidae: new subfamilies and paraphyly of most extant genera