Phylogenomics of Piranhas and Pacus (Serrasalmidae) Uncovers How Dietary Convergence and Parallelism Obfuscate Traditional Morphological Taxonomy

Phylogenomics, Lineage Diversification Rates, and the Evolution of Diadromy in Clupeiformes (Anchovies, Herrings, Sardines, and Relatives)

Migration independently evolved numerous times in animals, with a myriad of ecological and evolutionary implications. In fishes, perhaps the most extreme form of migration is diadromy, the migration between marine and freshwater environments. Key and long-standing questions are: how many times has diadromy evolved in fishes, how frequently do diadromous clades give rise to non-diadromous species, and does diadromy influence lineage diversification rates? Many diadromous fishes have large geographic ranges with constituent populations that use isolated freshwater habitats. This may limit gene flow between some populations, increasing the likelihood of speciation in diadromous lineages relative to nondiadromous lineages. Alternatively, diadromy may reduce lineage diversification rates if migration is associated with enhanced dispersal capacity that facilitates gene flow within and between populations. Clupeiformes (herrings, sardines, shads, and anchovies) is a model clade for testing hypotheses about the evolution of diadromy because it includes an exceptionally high proportion of diadromous species and several independent evolutionary origins of diadromy. However, relationships among major clupeiform lineages remain unresolved, and existing phylogenies sparsely sampled diadromous species, limiting the resolution of phylogenetically informed statistical analyses. We assembled a phylogenomic dataset and used multi-species coalescent and concatenation-based approaches to generate the most comprehensive, highly resolved clupeiform phylogeny to date, clarifying associations among several major clades and identifying recalcitrant relationships needing further examination. We determined that variation in rates of sequence evolution (heterotachy) and base-composition (nonstationarity) had little impact on our results. Using this phylogeny, we characterized evolutionary patterns of diadromy and tested for differences in lineage diversification rates between diadromous, marine, and freshwater lineages. We identified 13 transitions to diadromy, all during the Cenozoic Era (10 origins of anadromy, 2 origins of catadromy, and 1 origin of amphidromy), and 7 losses of diadromy. Two diadromous lineages rapidly generated nondiadromous species, demonstrating that diadromy is not an evolutionary dead end. We discovered considerably faster transition rates out of diadromy than to diadromy. The largest lineage diversification rate increase in Clupeiformes was associated with a transition to diadromy, but we uncovered little statistical support for categorically faster lineage diversification rates in diadromous versus nondiadromous fishes. We propose that diadromy may increase the potential for accelerated lineage diversification, particularly in species that migrate long distances. However, this potential may only be realized in certain biogeographic contexts, such as when diadromy allows access to ecosystems in which there is limited competition from incumbent species.

The piranha gut microbiome provides a selective lens into river water biodiversity

Advances in omics technologies have enabled the in-depth study of microbial communities and their metabolic profiles from all environments. Here metagenomes were sampled from piranha (Serrasalmus rhombeus) and from river water from the Rio São Benedito (Amazon Basin). Shotgun metagenome sequencing was used to explore diversity and to test whether fish microbiomes are a good proxy for river microbiome studies. The results showed that the fish microbiomes were not significantly different from the river water microbiomes at higher taxonomic ranks. However, at the genus level, fish microbiome alpha diversity decreased, and beta diversity increased. This result repeated for functional gene abundances associated with specific metabolic categories (SEED level 3). A clear delineation between water and fish was seen for beta diversity. The piranha microbiome provides a good and representative subset of its river water microbiome. Variations seen in beta biodiversity were expected and can be explained by temporal variations in the fish microbiome in response to stronger selective forces on its biodiversity. Metagenome assembled genomes construction was better from the fish samples. This study has revealed that the microbiome of a piranha tells us a lot about its river water microbiome and function.

Fishes (Actinopterygii) of the rapids and associated environments in the lower Vaupés River Basin: an undiscovered Colombian Amazon diversity

The Vaupés River stands out as one of the few within the Amazon basin due to its numerous rapids. These riverine fast-flowing sections not only provide habitat to highly specialized fishes but also function as natural barriers hindering the movement of fish along its course. During a fish-collecting expedition in the lower Vaupés River basin in Colombia, 95 species were registered belonging to 30 families and seven orders. Despite recent inventories in the region, our comprehensive sampling efforts particularly focused on the rapids and associated rheophilic fauna, allowing us to contribute the first records of four fish species in Colombia (Mylopluslucienae Andrade, Ota, Bastos & Jégu, 2016, Tometesmakue Jégu, Santos & Jégu, 2002, also first record of the genus, Leptodoraspraelongus (Myers & Weitzman, 1956), and Eigenmanniamatintapereira Peixoto, Dutra & Wosiacki, 2015) and six presumably undescribed species (i.e., Jupiaba sp., Moenkhausia sp., Phenacogaster sp., Bunocephalus sp., Hemiancistrus sp., and Archolaemus sp.). In this study, a commented list of the ichthyofauna of these environments is presented, as well as a photographic catalog of fish species integrated into the CaVFish Project - Colombia.

Dental Dynamics: A Fast New Tool for Quantifying Tooth and Jaw Biomechanics in 3D Slicer

Teeth reveal how organisms interact with their environment. Biologists have long looked at the diverse form and function of teeth to study the evolution of feeding, fighting, and development. The exponential rise in the quantity and accessibility of computed tomography (CT) data has enabled morphologists to study teeth at finer resolutions and larger macroevolutionary scales. Measuring tooth function is no easy task, in fact, much of our mechanical understanding is derived from dental shape. Categorical descriptors of tooth shape such as morphological homodonty and heterodonty, overlook nuances in function by reducing tooth diversity for comparative analysis. The functional homodonty method quantitatively assesses the functional diversity of whole dentitions from tooth shape. This method uses tooth surface area and position to calculate the transmission of stress and estimates a threshold for functionally homodont teeth through bootstrapping and clustering techniques. However, some vertebrates have hundreds or thousands of teeth and measuring the shape and function of every individual tooth can be a painstaking task. Here, we present Dental Dynamics, a module for 3D Slicer that allows for the fast and precise quantification of dentitions and jaws. The tool automates the calculation of several tooth traits classically used to describe form and function (i.e., aspect ratio, mechanical advantage, force, etc.). To demonstrate the usefulness of our module we used Dental Dynamics to quantify 780 teeth across 20 salamanders that exhibit diverse ecologies. We coupled these data with the functional homodonty method to investigate the hypothesis that arboreal Aneides salamanders have novel tooth functions. Dental Dynamics provides a new and fast way to measure teeth and increases the accessibility of the functional homodonty method. We hope Dental Dynamics will encourage further theoretical and methodological development for quantifying and studying teeth.

Chromosomal characterization of three species of Serrasalmini (Serrasalmidae: Characiformes)

The tribe Serrasalmini is a diverse group with paraphyletic genera and taxonomic uncertainties. Several studies have been carried out in this group of fish in order to understand this problem, including the cytogenetic approach. In this study, three species of a clade of Serrasalmini were characterized cytogenetically - Pristobrycon striolatus, Catoprion absconditus and Pygopristis denticulatus. The three species presented diploid number (2n) equal to 62 chromosomes, of one and two arms, with karyotypic formulas and species-specific fundamental numbers. Heterochromatin is centromeric and terminal (bi-telomeric) in most chromosomes, with a conspicuous interstitial block at pair 1 (m) in all three species. The nucleolar organizer regions were multiple and C-band positive, and their location was confirmed via 18S ribosomal DNA mapping; however, with additional sites. The 5S rDNA was located in interstitial region of long arm of pair 1 (m), in the three species (homeologous). Moreover, we observed synteny between 18S and 5S in the species C. absconditus and P. denticulatus, which, according to fiber-FISH, are interspersed. Thus, the maintenance of 2n (62) evidences the diversification of chromosomal formulas within the clade by non-Robertsonian rearrangements and reflects the paraphyly of the related species.

Macroevolutionary consequences of karyotypic changes in the neotropical Serrasalmidae fishes (Ostariophysi, Characiformes) diversification

In the Neotropical region, one of the most diverse families of freshwater fishes is the monophyletic Serrasalmidae. Karyotypically, the family shows high diversity in chromosome numbers (2n = 54 to 64). However, little is discussed about whether the chromosomal changes are associated with cladogenetic events within this family. In the present study, we evaluated the role of chromosomal changes in the evolutionary diversification of Serrasalmidae. Our phylogenetic sampling included 36 species and revealed three main clades. The ancestral chromosome number reconstruction revealed the basic number 2n = 54 and a high frequency of ascending dysploid events in the most derived lineages. Our biogeographic reconstruction suggests an Amazonian origin of the family at 48-38 Mya, with independent colonization of other basins between 15 and 8 Mya. We did not find specific chromosomal changes or increased diversification rates correlated with the colonization of a new environment. On the other hand, an increase in the diversification rate was detected involving the genus Serrasalmus and Pygocentrus in the Miocene, correlated with the stasis of 2n = 60. Our data demonstrate that chromosomal rearrangements might have played an important evolutionary role in major cladogenetic events in Serrasalmidae, revealing them as a possible evolutionary driver in their diversification.

Phylogenomics, evolution of trophic traits and divergence times of hemiodontid fishes (Ostariophysi: Characiformes)

The South American characiform family Hemiodontidae comprises five genera and 34 species. The family lacks comprehensive phylogenetic hypotheses resolving its species relationships. The studies that addressed these questions exhibited a narrow taxon sampling or used single-locus markers. Herein we surveyed hundreds of ultraconserved elements (UCEs) loci to provide the first molecular phylogenetic hypothesis and divergence time estimates for hemiodontids encompassing all its genera and most species (27 of the 34 valid species). We also tracked the history of the protractile upper jaw in the genera Argonectes and Bivibranchia across the recovered phylogenies through ancestral state reconstruction. Our results corroborate the monophyly of Hemiodontidae and the genera Argonectes and Bivibranchia in all phylogenetic methods with maximum clade support. The genera Anodus and Hemiodus were not monophyletic because Anodus elongatus was sister to the monotypic Micromischodus instead of A. orinocensis, and H. immaculatus did not form a clade with its other congeners, but instead was sister to the clade including Anodus and Micromischodus. All remaining species of Hemiodus were placed together into a monophyletic group, where they were arranged into four major subclades. The relationship in the family is summarised as: (Bivibranchia, (Argonectes, ((H. immaculatus, (Anodus, Micromischodus)), Hemiodus clade))), in discordance with the morphological phylogeny that placed all genera monophyletic and resolved the family as: ((Anodus, Micromischodus), (Hemiodus, (Argonectes, Bivibranchia))). The origin of Hemiodontidae was estimated from the Late Cretaceous to the Middle Paleogene, with the mean age in the Paleocene, while the origin of most hemiodontid genera except Bivibranchia occurred in the Miocene. Unordered parsimony and likelihood reconstruction indicates that Argonectes and Bivibranchia developed their protractile upper jaw independently.

Lip service: Histological phenotypes correlate with diet and feeding ecology in herbivorous pacus

Complex prey processing requires the repositioning of food between the teeth, as modulated by a soft tissue appendage like a tongue or lips. In this study, we trace the evolution of lips and ligaments, which are used during prey capture and prey processing in an herbivorous group of fishes. Pacus (Serrasalmidae) are Neotropical freshwater fishes that feed on leaves, fruits, and seeds. These prey are hard or tough, require high forces to fracture, contain abrasive or caustic elements, or deform considerably before failure. Pacus are gape-limited and do not have the pharyngeal jaws many bony fishes use to dismantle and/or transport prey. Despite their gape limitation, pacus feed on prey larger than their mouths, relying on robust teeth and a hypertrophied lower lip for manipulation and breakdown of food. We used histology to compare the lip morphology across 14 species of pacus and piranhas to better understand this soft tissue. We found that frugivorous pacus have larger, more complex lips which are innervated and folded at their surface, while grazing species have callused, mucus-covered lips. Unlike mammalian lips or tongues, pacu lips lack any intrinsic skeletal or smooth muscle. This implies that pacu lips lack dexterity; however, we found a novel connection to the primordial ligament which suggests that the lips are actuated by the jaw adductors. We propose that pacus combine hydraulic repositioning of prey inside the buccal cavity with direct oral manipulation, the latter using a combination of a morphologically heterodont dentition and compliant lips for reorienting food.

Early ontogeny of the commercially valuable fish red-bellied pacu Piaractus brachypomus (Characiformes, Serrasalmidae) from the Amazon, Brazil

The initial development of the red-bellied pacu Piaractus brachypomus is described using morphological, meristic and morphometric characteristics. A total of 127 individuals were analysed (47 in the yolk-sac, 35 in pre-flexion, five in flexion, 20 in post-flexion and 20 in juvenile) with standard length varying between 2.92 and 48.61 mm. The larvae are born poorly developed and have a discoidal yolk at ~6.33 mm standard length. During early ontogeny, the mouth passes from terminal to subterminal and the anal opening reaches the vertical line over the midline region of the body. There are changes in body shape from long and moderate to deep, head length from small to large, and eye diameter from moderate to large. Dendritic chromatophores were present in the ventral, dorsal and upper part of the swim bladder in the early larval stages. Rounded spots are evident all over the body in juveniles. The total number of myomeres ranges from 39 to 41 (20-23 pre-anal, 17-20 post-anal). Through the morphometric relationships, it was evidenced that the greatest changes during the initial ontogeny of P. brachypomus occur in the transition from the post-flexion stage to the juvenile period, indicating changes in behaviour, foraging and physiology.

The Satellite DNA Catalogues of Two Serrasalmidae (Teleostei, Characiformes): Conservation of General satDNA Features over 30 Million Years

Satellite DNAs (satDNAs) are tandemly repeated sequences that are usually located on the heterochromatin, and the entire collection of satDNAs within a genome is called satellitome. Primarily, these sequences are not under selective pressure and evolve by concerted evolution, resulting in elevated rates of divergence between the satDNA profiles of reproductive isolated species/populations. Here, we characterized two additional satellitomes of Characiformes fish (Colossoma macropomum and Piaractus mesopotamicus) that diverged approximately 30 million years ago, while still retaining conserved karyotype features. The results we obtained indicated that several satDNAs (50% of satellite sequences in P. mesopotamicus and 43% in C. macropomum) show levels of conservation between the analyzed species, in the nucleotide and chromosomal levels. We propose that long-life cycles and few genomic changes could slow down rates of satDNA differentiation.

Paleogene emergence and evolutionary history of the Amazonian fossorial fish genus Tarumania (Teleostei: Tarumaniidae)

Tarumania walkerae is a rare fossorial freshwater fish species from the lower Rio Negro, Central Amazonia, composing the monotypic and recently described family Tarumaniidae. The family has been proposed as the sister group of Erythrinidae by both morphological and molecular studies despite distinct arrangements of the superfamily Erythrinoidea within Characiformes. Recent phylogenomic studies and time-calibrated analyses of characoid fishes have not included specimens of Tarumania in their analyses. We obtained genomic data for T. walkerae and constructed a phylogeny based on 1795 nuclear loci with 488,434 characters of ultraconserved elements (UCEs) for 108 terminals including specimens of all 22 characiform families. The phylogeny confirms the placement of Tarumaniidae as sister to Erythrinidae but differs from the morphological hypothesis in the placement of the two latter families as sister to the clade with Hemiodontidae, Cynodontidae, Serrasalmidae, Parodontidae, Anostomidae, Prochilodontidae, Chilodontidae, and Curimatidae. The phylogeny calibrated with five characoid fossils indicates that Erythrinoidea diverged from their relatives during the Late Cretaceous circa 90 Ma (108–72 Ma), and that Tarumania diverged from the most recent common ancestor of Erythrinidae during the Paleogene circa 48 Ma (66–32 Ma). The occurrence of the erythrinoid-like †Tiupampichthys in the Late Cretaceous–Paleogene formations of the El Molino Basin of Bolivia supports our hypothesis for the emergence of the modern Erythrinidae and Tarumaniidae during the Paleogene.

Divergence times of the Rhoadsia clade (Characiformes: Characidae)

Abstract The family Characidae is the most diverse group of fishes in the Neotropics with challenging systematics. The three genera Carlana, Parastremma, and Rhoadsia, formerly considered the subfamily Rhoadsiinae, are now included in the subfamily Stethaprioninae. Previous phylogenetic analyses did not include all genera of Rhoadsiinae, specifically Parastremma. Here, we estimated the phylogenetic relationships and divergence times of the genera of Rhoadsiinae (the Rhoadsia clade) relative to the most representative genera of the Characidae. We used six molecular markers from the mitochondrial and nuclear genome to estimate the phylogeny and divergence times. We confirmed the monophyly of the Rhoadsia clade. Furthermore, we estimated that the Central American genus Carlana and the western Colombian genus Parastremma diverged approximately 13 Mya (95% HPD 8.36–18.11), consistent with the early-closure estimates of the Isthmus of Panama (~15 Mya). The genus Rhoadsia, endemic to Western Ecuador and Northern Peru, was estimated to originate at around 20 Mya (95% HPD 14.35–25.43), consistent with the Andean uplift (~20 Mya).

Early development of two commercially valuable fish from the lower Amazon River, Brazil (Characiformes: Serrasalmidae)

Abstract We described the early development of Myloplus asterias and M. lobatus, two fish species of the Serrasalmidae using morphological, meristic, and morphometric characteristics. These herbivores serrasalmids are heavily fished because of their commercial importance in the Amazon. The individuals were collected between 2016 and 2020 in the limnetic zone of open water and macrophyte stands in the Lower Amazon River floodplain. We tested different growth models to identify the development pattern of these species. During the initial ontogeny, these two species can be differentiated mainly by the myomeres total number, 37 to 39 in M. asterias vs. 40 to 41 in M. lobatus, the pigmentation pattern, and dorsal-fin ray numbers. These characteristics are effective in distinguishing these species from other serrasalmids. The morphometric relationships were also different between these two species, showing distinct patterns in growth between the analyzed features. An identification key for larvae of some sympatric Serrasalmidae species from the Amazon basin is presented. Our expectation is that this study will contribute to the knowledge of the initial ontogeny and the biology of fish species in the Neotropical region.

Comparative cytogenetics of Serrasalmidae (Teleostei: Characiformes): The relationship between chromosomal evolution and molecular phylogenies

Serrasalmidae has high morphological and chromosomal diversity. Based on molecular hypotheses, the family is currently divided into two subfamilies, Colossomatinae and Serrasalminae, with Serrasalminae composed of two tribes: Myleini (comprising most of pacus species) and Serrasalmini (represented by Metynnis, Catoprion, and remaining piranha’s genera). This study aimed to analyze species of the tribes Myleini (Myloplus asterias, M. lobatus, M. rubripinnis, M. schomburgki, and Tometes camunani) and Serrasalmini (Metynnis cuiaba, M. hypsauchen, and M. longipinnis) using classical and molecular cytogenetic techniques in order to understand the chromosomal evolution of the family. The four species of the genus Myloplus and T. camunani presented 2n = 58 chromosomes, while the species of Metynnis presented 2n = 62 chromosomes. The distribution of heterochromatin occurred predominantly in pericentromeric regions in all species. Tometes camunani and Myloplus spp. presented only one site with 5S rDNA. Multiple markers of 18S rDNA were observed in T. camunani, M. asterias, M. lobatus, M. rubripinnis, and M. schomburgkii. For Metynnis, however, synteny of the 18S and 5S rDNA was observed in the three species, in addition to an additional 5S marker in M. longipinnis. These data, when superimposed on the phylogeny of the family, suggest a tendency to increase the diploid chromosome number from 54 to 62 chromosomes, which occurred in a nonlinear manner and is the result of several chromosomal rearrangements. In addition, the different karyotype formulas and locations of ribosomal sequences can be used as cytotaxonomic markers and assist in the identification of species.

Colossoma macropomum-A tropical fish model for biology and aquaculture

Tambaqui, a species native to the Amazon and Orinoco Basins and their tributaries, has a history marked by biological resilience that makes this species a model for studies focused on ecology, physiology, and fish farming. In addition, it is of economic interest, due to its favorable characteristics for production in farms and its unique flavor. As the tambaqui responds in a unique way to several environmental disturbances of natural origin, the species is often used in environmental studies. Some of these studies have been revisited in this review. We revised aspects related to its natural history, habitats and geographic distribution, physiological and biochemical adaptations, and zootechnical performance. The extraordinary adaptation of the tambaqui is the fast expansion of its lower lip when exposed to low oxygen availability that is improved simultaneously with other adjustments. The resilience of this species to significant alterations in water pH is also surprising, and is incomparable with that of other species, as only when it is exposed to pH 3.5, does the tambaqui begin to present physiological-biochemical disturbances. The analysis of the gene expression of tambaqui specimens under different experimental conditions has shed light on the adaptive mechanisms used by this unique Amazonian species. In this sense, this review sought to gather information regarding the tambaqui, and its many biological features employed to survive environmental challenges.

Hyperspectral data as a biodiversity screening tool can differentiate among diverse Neotropical fishes

Hyperspectral data encode information from electromagnetic radiation (i.e., color) of any object in the form of a spectral signature; these data can then be used to distinguish among materials or even map whole landscapes. Although hyperspectral data have been mostly used to study landscape ecology, floral diversity and many other applications in the natural sciences, we propose that spectral signatures can be used for rapid assessment of faunal biodiversity, akin to DNA barcoding and metabarcoding. We demonstrate that spectral signatures of individual, live fish specimens can accurately capture species and clade-level differences in fish coloration, specifically among piranhas and pacus (Family Serrasalmidae), fishes with a long history of taxonomic confusion. We analyzed 47 serrasalmid species and could distinguish spectra among different species and clades, with the method sensitive enough to document changes in fish coloration over ontogeny. Herbivorous pacu spectra were more like one another than they were to piranhas; however, our method also documented interspecific variation in pacus that corresponds to cryptic lineages. While spectra do not serve as an alternative to the collection of curated specimens, hyperspectral data of fishes in the field should help clarify which specimens might be unique or undescribed, complementing existing molecular and morphological techniques.

The B Chromosomes of Prochilodus lineatus (Teleostei, Characiformes) Are Highly Enriched in Satellite DNAs

B or supernumerary chromosomes are dispensable elements that are widely present in numerous eukaryotes. Due to their non-recombining nature, there is an evident tendency for repetitive DNA accumulation in these elements. Thus, satellite DNA plays an important role in the evolution and diversification of B chromosomes and can provide clues regarding their origin. The characiform Prochilodus lineatus was one of the first discovered fish species bearing B chromosomes, with all populations analyzed so far showing one to nine micro-B chromosomes and exhibiting at least three morphological variants (Ba, Bsm, and Bm). To date, a single satellite DNA is known to be located on the B chromosomes of this species, but no information regarding the differentiation of the proposed B-types is available. Here, we characterized the satellitome of P. lineatus and mapped 35 satellite DNAs against the chromosomes of P. lineatus, of which six were equally located on all B-types and this indicates a similar genomic content. In addition, we describe, for the first time, an entire population without B chromosomes.

Accelerated Diversification Explains the Exceptional Species Richness of Tropical Characoid Fishes

The Neotropics harbor the most species-rich freshwater fish fauna on the planet, but the timing of that exceptional diversification remains unclear. Did the Neotropics accumulate species steadily throughout their long history, or attain their remarkable diversity recently? Biologists have long debated the relative support for these museum and cradle hypotheses, but few phylogenies of megadiverse tropical clades have included sufficient taxa to distinguish between them. We used 1,288 ultraconserved element loci (UCE) spanning 293 species, 211 genera and 21 families of characoid fishes to reconstruct a new, fossil-calibrated phylogeny and infer the most likely diversification scenario for a clade that includes a third of Neotropical fish diversity. This phylogeny implies paraphyly of the traditional delimitation of Characiformes because it resolves the largely Neotropical Characoidei as the sister lineage of Siluriformes (catfishes), rather than the African Citharinodei. Time-calibrated phylogenies indicate an ancient origin of major characoid lineages and reveal a much more recent emergence of most characoid species. Diversification rate analyses infer increased speciation and decreased extinction rates during the Oligocene at around 30 million years ago (Ma) during a period of mega-wetland formation in the proto-Orinoco-Amazonas. Three species-rich and ecomorphologically diverse lineages (Anostomidae, Serrasalmidae, and Characidae) that originated more than 60 Ma in the Paleocene experienced particularly notable bursts of Oligocene diversification and now account collectively for 68% of the approximately 2,150 species of Characoidei. In addition to paleogeographic changes, we discuss potential accelerants of diversification in these three lineages. While the Neotropics accumulated a museum of ecomorphologically diverse characoid lineages long ago, this geologically dynamic region also cradled a much more recent birth of remarkable species-level diversity.

Use of bioacoustics in species identification: Piranhas from genus Pygocentrus (Teleostei: Serrasalmidae) as a case study

The genus Pygocentrus contains three valid piranha species (P. cariba, P. nattereri and P. piraya) that are allopatric in tropical and subtropical freshwater environments of South America. This study uses acoustic features to differentiate the three species. Sounds were recorded in P. cariba, two populations of P. nattereri (red- and yellow-bellied) and P. piraya; providing sound description for the first time in P. cariba and P. piraya. Calls of P. cariba were distinct from all the other studied populations. Red- and yellow-bellied P. nattereri calls were different from each other but yellow-bellied P. nattereri calls were similar to those of P. piraya. These observations can be explained by considering that the studied specimens of yellow-bellied P. nattereri have been wrongly identified and are actually a sub-population of P. piraya. Morphological examinations and recent fish field recordings in the Araguari River strongly support our hypothesis. This study shows for the first time that sounds can be used to discover identification errors in the teleost taxa.