Richard P. Vari

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

BackgroundWith 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.ResultsIn 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.ConclusionA 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.

Taxonomic Impediment or Impediment to Taxonomy? A Commentary on Systematics and the Cybertaxonomic-Automation Paradigm

Marcelo R. de Carvalho AE Flavio A. Bockmann AE Dalton S. Amorim AE Carlos Roberto F. Brandao AE Mario de Vivo AE Jose L. de Figueiredo AE Heraldo A. Britski AE Mario C. C. de Pinna AE Naercio A. Menezes AE Fernando P. L. Marques AE Nelson Papavero AE Eliana M. Cancello AE Jorge V. Crisci AE John D. McEachran AE Robert C. Schelly AE John G. Lundberg AE Anthony C. Gill AE Ralf Britz AE Quentin D. Wheeler AE Melanie L. J. Stiassny AE Lynne R. Parenti AE Larry M. Page AE Ward C. Wheeler AE Julian Faivovich AE Richard P. Vari AE Lance Grande AE Chris J. Humphries AE Rob DeSalle AE Malte C. Ebach AE Gareth J. Nelson

Genome-wide interrogation advances resolution of recalcitrant groups in the tree of life

Much progress has been achieved in disentangling evolutionary relationships among species in the tree of life, but some taxonomic groups remain difficult to resolve despite increasing availability of genome-scale data sets. Here we present a practical approach to studying ancient divergences in the face of high levels of conflict, based on explicit gene genealogy interrogation (GGI). We show its efficacy in resolving the controversial relationships within the largest freshwater fish radiation (Otophysi) based on newly generated DNA sequences for 1,051 loci from 225 species. Initial results using a suite of standard methodologies revealed conflicting phylogenetic signal, which supports ten alternative evolutionary histories among early otophysan lineages. By contrast, GGI revealed that the vast majority of gene genealogies supports a single tree topology grounded on morphology that was not obtained by previous molecular studies. We also reanalysed published data sets for exemplary groups with recalcitrant resolution to assess the power of this approach. GGI supports the notion that ctenophores are the earliest-branching animal lineage, and adds insight into relationships within clades of yeasts, birds and mammals. GGI opens up a promising avenue to account for incompatible signals in large data sets and to discern between estimation error and actual biological conflict explaining gene tree discordance.

The jaw adductor muscle complex in teleostean fishes: evolution, homologies and revised nomenclature (osteichthyes: actinopterygii).

The infraclass Teleostei is a highly diversified group of bony fishes that encompasses 96% of all species of living fishes and almost half of extant vertebrates. Evolution of various morphological complexes in teleosts, particularly those involving soft anatomy, remains poorly understood. Notable among these problematic complexes is the adductor mandibulae, the muscle that provides the primary force for jaw adduction and mouth closure and whose architecture varies from a simple arrangement of two segments to an intricate complex of up to ten discrete subdivisions. The present study analyzed multiple morphological attributes of the adductor mandibulae in representatives of 53 of the 55 extant teleostean orders, as well as significant information from the literature in order to elucidate the homologies of the main subdivisions of this muscle. The traditional alphanumeric terminology applied to the four main divisions of the adductor mandibulae – A1, A2, A3, and Aω – patently fails to reflect homologous components of that muscle across the expanse of the Teleostei. Some features traditionally used as landmarks for identification of some divisions of the adductor mandibulae proved highly variable across the Teleostei; notably the insertion on the maxilla and the position of muscle components relative to the path of the ramus mandibularis trigeminus nerve. The evolutionary model of gain and loss of sections of the adductor mandibulae most commonly adopted under the alphanumeric system additionally proved ontogenetically incongruent and less parsimonious than a model of subdivision and coalescence of facial muscle sections. Results of the analysis demonstrate the impossibility of adapting the alphanumeric terminology so as to reflect homologous entities across the spectrum of teleosts. A new nomenclatural scheme is proposed in order to achieve congruence between homology and nomenclature of the adductor mandibulae components across the entire Teleostei.

The Neotropical whale catfishes (Siluriformes: Cetopsidae: Cetopsinae), a revisionary study

The catfishes of the subfamily Cetopsinae of the Neotropical family Cetopsidae are revised. Four genera, Cetopsidium new genus, Cetopsis, Denticetopsis, and Paracetopsis Bleeker are recognized as valid. Bathycetopsis, Hemicetopsis, and Pseudocetopsis are considered synonyms of Cetopsis and Paracetopsis Eigenmann & Bean and Cetopsogiton synonyms of Paracetopsis. Thirty-seven species are recognized in the Cetopsinae. Cetopsidium includes six species: C. ferreirai, new species, rio Trombetas; C. minutum, Essequibo River; C. morenoi, central and western portions of rio Orinoco; C. orientale, coastal rivers of Suriname and French Guiana, and tentatively rio Tocantins and rio Xingu; C. pemon, new species, rio Caura, rio Caroni, rio Meta, and rio Branco; and C. roae, new species, Rupununi River. Cetopsis includes 21 species: C. amphiloxa, rio San Juan, rio Atrato, and rio Patia, western Colombia, and rivers of northwestern Ecuador; C. arcana, new species, rio Tocantins; C. baudoensis, rio Baudo; C. caiapo, new species, rio Tocantins; C. candiru, Amazon basin; C. fimbriata, new species, rio Truando; C. coecutiens, rio Amazonas, rio Tocantins, and rio Orinoco; C. gobioides, upper rio Sao Francisco, rio Parana, rio Uruguay, and rio Juquia; C. jurubidae, rio Jurubida; C. montana, new species, western portions of Amazon basin; C. motatanensis, Lago Maracaibo basin; C. oliveirai, Amazon basin; C. orinoco, rio Orinoco, rio Aroa, and rio Yaracuy; C. othonops, rio Magdalena and rio Sinu; C. parma, western Amazon basin; C. pearsoni, new species, upper portions of rio Madeira; C. plumbea, western portions of rio Amazonas; C. sandrae, new species, rio Tapajos; C. sarcodes, new species, rio Tocantins; C. starnesi, new species, northwestern rio de La Plata and southern rio Madeira; and C. umbrosa, new species, western rio Orinoco. Cetopsis chalmersi is a synonym of C. gobioides. Cetopsis macroteronema is a synonym of C. plumbea. Denticetopsis includes seven species: D. epa, new species, rio Tocantins; D. iwokrama, new species, Siparuni River; D. macilenta, Potaro River; D. praecox, rio Baria; D. royeroi, upper rio Negro; D. sauli, upper rio Negro; and D. seducta, new species, western portions of rio Amazonas and rio Orinoco. Paracetopsis consists of three species: P. atahualpa, new species, rio Tumbes, northwestern Peru, and rio Zarumilla, southwestern Ecuador; P. bleekeri, rio Guayas and rio Santa Rosa, south-western Ecuador; and P. esmeraldas, new species, rivers of northwestern Ecuador. Cetopsis ventralis and C. occidentalis are synonyms of Paracetopsis bleekeri. A neotype is designated for Paracetopsis bleekeri. Lectotypes are designated for Cetopsis candiru, Cetopsis chalmersi, and Cetopsis plumbeus.

Cryptic species in the Neotropical fish genus Curimatopsis (Teleostei, Characiformes)

Detritivores of the fish family Curimatidae are assigned to eight genera, one of which, the Curimatopsis, with only five species, is the least speciose genus and sister to other seven genera in the family. Ongoing morphological investigations reveal, however, the likely existence of additional species. In this study, fifty‐one specimens of Curimatopsis from multiple rivers of the Amazon, Paraguay and Suriname drainages were identified morphologically according to the present species concepts and then barcoded using the universal cytochrome c oxidase subunit I (COI) mitochondrial marker. Species delimitation analyses were conducted using Bayesian methods through the general mixed Yule‐coalescent analysis combined with conventional likelihood, genetic distance and haplotypic diversity approaches. We found eleven well‐supported clusters that represent four of the named species and seven cryptic, undescribed species of Curimatopsis. Our results show a clear delimitation of species boundaries constrained by distinct Amazonian river ecotones that may have promoted intrageneric lineage diversification. This is the first of a series of genetic studies applicable to future taxonomic, phylogenetic and evolutionary studies across the Curimatidae.

New Species of Trichomycterus (Teleostei: Siluriformes: Trichomycteridae) Lacking a Pelvic Fin and Girdle from the Andes of Argentina

Abstract Trichomycterus catamarcensis, new species, is described from a tributary to the high elevation Laguna Blanca in Departamento Belén, Provincia de Catamarca, Argentina. Characters from various body systems indicate that the new species is a member of the subfamily Trichomycterinae. The new species is separable from the other members of the Trichomycterinae by its lack of the pelvic fins and girdle, the form of the body and caudal fin, the number of dorsal fin rays and ribs, its pigmentation pattern, the form of premaxillary dentition, and the maximum body size. Trichomycterus catamarcensis, nueva especie, es descripta de un tributario de Laguna Blanca de elevada altura en el Departamento Belén, Provincia de Catamarca, Argentina. Caracteres de varios sistemas del cuerpo indican que la nueva especie es un miembro de la subfamilia Trichomycterinae. La nueva especie se separa de los otros miembros de Trichomycterinae por su ausencia de aletas pélvicas y cintura pélvica, la forma del cuerpo y aleta caudal, el número de radios de la aleta dorsal y costillas, su patrón de pigmentación, la forma de la dentición premaxilar y el tamaño máximo del cuerpo.

New Species of Astyanax (Ostariophysi: Characiformes: Characidae) from the Upper Rio Paraná System, Brazil

Abstract Astyanax bockmanni, a new species of characid, is widespread in streams in the upper Rio Paraná system of central, southeastern, and southern Brazil. Samples of the species were identified by previous authors as A. eigenmanniorum, a species originally described from far southern Brazil. Astyanax bockmanni differs from A. eigenmanniorum and all congeners in the combination of morphometric, meristic, and pigmentary features and details of oral dentition. Uncertainties concerning the generic placement of Astyanax paranahybae are discussed, and it is proposed that the species is a member of a clade within the Characidae that does not include Astyanax. Astyanax bockmanni, uma nova espécie de caracídeo, é amplamente distribuída em riachos do Alto Rio Paraná, nas regiões centro-oeste, sudeste e sul do Brasil. Amostras dessa espécie foram previamente identificadas por diversos autores como A. eigenmanniorum, uma espécie originalmente descrita do extremo sul do Brasil. Astyanax bockmanni difere de A. eigenmanniorum e demais congêneres por uma combinação de caracteres morfométricos e de pigmentação, além de detalhes da dentição oral. Incertezas quanto ao posicionamento genérico de Astyanax paranahybae são discutidas e propõe-se que a espécie seja membro de um clado de Characidae que não inclui Astyanax.

Molecular phylogenetics of the Neotropical fish family Prochilodontidae (Teleostei: Characiformes).

Migratory detritivores of the characiform family Prochilodontidae occur throughout the freshwaters of much of South America. Prochilodontids often form massive populations and many species achieve substantial body sizes; a combination that makes them one of the most commercially important fish groups on the continent. Their economic significance notwithstanding, prochilodontids have never been the subject of a comprehensive molecular phylogenetic analysis. Using three mitochondrial and three nuclear loci spanning all prochilodontid species, we generated a novel phylogenetic hypothesis for the family. Our results strongly support monophyly of the family and the three included genera. A novel, highly supported placement of Ichthyoelephas sister to the clade containing Prochilodus and Semaprochilodus diverges from a previous morphological hypothesis. Most previously hypothesized interspecific relationships are corroborated and some longstanding polytomies within Prochilodus and Semaprochilodus are resolved. The morphologically similar P. brevis, P. lacustris, P. nigricans and P. rubrotaeniatus are embedded within what is herein designated as the P. nigricans group. Species limits and distributions of these species are problematic and the group clearly merits taxonomic revision.

New Species of Trichomycterus from the Andean Cordillera of Argentina (Siluriformes: Trichomycteridae)

Abstract Trichomycterus hualco, new species, is described from an Andean stream in the Provincia de La Rioja, Argentina. The new species is distinguished from other species of Trichomycterus in the combination of the number of odontodes on the opercle and interopercle, the degree of exposure of the odontodes on the interopercle, the form of the premaxillary teeth, the presence of papillae-like structures on the body, the number of vertebrae, the position of the first proximal dorsal-fin pterygiophore, the form of the supraorbital canal within the frontal, the length of the lateral-line canal, and various meristic features.