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Nogueira AF, Oliveira C, Langeani F, Netto-Ferreira AL. Phylogenomics, evolution of trophic traits and divergence times of hemiodontid fishes (Ostariophysi: Characiformes). Mol Phylogenet Evol 2023:107864. [PMID: 37343656 DOI: 10.1016/j.ympev.2023.107864] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Revised: 06/08/2023] [Accepted: 06/16/2023] [Indexed: 06/23/2023]
Abstract
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.
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Affiliation(s)
- Acácio F Nogueira
- Programa de Pós-Graduação em Zoologia, Instituto de Ciências Biológicas, Universidade Federal do Pará and Museu Paraense Emílio Goeldi, Rua Augusto Corrêa, 01, 66075-110, Belém, PA, Brazil; Laboratório de Biologia e Genética de Peixes, Departamento de Biologia Estrutural e Funcional, Instituto de Biociências, Universidade Estadual Paulista, Rua Prof. Dr. Antonio C. W. Zanin, 250, 18618-689, Botucatu, SP, Brazil; Laboratório de Ictiologia, Departamento de Zoologia, Instituto de Biociências, Universidade Federal do Rio Grande do Sul, Avenida Bento Gonçalves, 9500, 91501-970, Porto Alegre, RS, Brazil.
| | - Claudio Oliveira
- Laboratório de Biologia e Genética de Peixes, Departamento de Biologia Estrutural e Funcional, Instituto de Biociências, Universidade Estadual Paulista, Rua Prof. Dr. Antonio C. W. Zanin, 250, 18618-689, Botucatu, SP, Brazil.
| | - Francisco Langeani
- Departamento de Ciências Biológicas, Instituto de Biociências, Letras e Ciências Exatas, Universidade Estadual Paulista, Rua Cristóvão Colombo, 2265, 15054-000, São José do Rio Preto, SP, Brazil.
| | - André L Netto-Ferreira
- Laboratório de Ictiologia, Departamento de Zoologia, Instituto de Biociências, Universidade Federal do Rio Grande do Sul, Avenida Bento Gonçalves, 9500, 91501-970, Porto Alegre, RS, Brazil.
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Souza CS, Mattox GMT, Vita G, Ochoa LE, Melo BF, Oliveira C. Molecular species delimitation and description of a new species of Phenacogaster (Teleostei, Characidae) from the southern Amazon basin. Zookeys 2023; 1164:1-21. [PMID: 37273974 PMCID: PMC10239021 DOI: 10.3897/zookeys.1164.102436] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Accepted: 04/27/2023] [Indexed: 06/06/2023] Open
Abstract
Phenacogaster is the most species-rich genus of the subfamily Characinae with 23 valid species broadly distributed in riverine systems of South America. Despite the taxonomic diversity of the genus, little has been advanced about its molecular diversity. A recent molecular phylogeny indicated the presence of undescribed species within Phenacogaster that is formally described here. We sampled 73 specimens of Phenacogaster and sequenced the mitochondrial cytochrome c oxidase subunit I (COI) gene in order to undertake species delimitation analyses and evaluate their intra- and interspecific genetic diversity. The results show the presence of 14 species, 13 of which are valid and one undescribed. The new species is known from the tributaries of the Xingu basin, the Rio das Mortes of the Araguaia basin, and the Rio Teles Pires of the Tapajós basin. It is distinguished by the incomplete lateral line, position of the humeral blotch near the pseudotympanum, and shape of the caudal-peduncle blotch. Meristic data and genetic differentiation relative to other Phenacogaster species represent strong evidence for the recognition of the new species and highlight the occurrence of an additional lineage of P.franciscoensis.
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Affiliation(s)
- Camila S. Souza
- Departamento de Biologia Estrutural e Funcional, Instituto de Biociências, Universidade Estadual Paulista, R. Prof. Dr. Antônio C. W. Zanin 250, 18618-689, Botucatu, SP, BrazilUniversidade Estadual PaulistaBotucatuBrazil
| | - George M. T. Mattox
- Laboratório de Ictiologia de Sorocaba, Departamento de Biologia, Universidade Federal de São Carlos, Rod. João Leme dos Santos km 110, 18052-780, Sorocaba, SP, BrazilUniversidade Federal de São CarlosSorocabaBrazil
| | - George Vita
- Museu de Zoologia da Universidade de São Paulo, Av. Nazaré 481, 04218-970, São Paulo, SP, BrazilMuseu de Zoologia da Universidade de São PauloSão PauloBrazil
| | - Luz E. Ochoa
- Dirección Académica, Universidad Nacional de Colombia, Sede de La Paz, Km 9 Via Valledupar, Los Robles La Paz, Cesar, ColombiaUniversidad Nacional de ColombiaLos Robles La PazColombia
| | - Bruno F. Melo
- Department of Ichthyology, American Museum of Natural History, 200 Central Park West, New York, NY 10024, USAAmerican Museum of Natural HistoryNew YorkUnited States of America
| | - Claudio Oliveira
- Departamento de Biologia Estrutural e Funcional, Instituto de Biociências, Universidade Estadual Paulista, R. Prof. Dr. Antônio C. W. Zanin 250, 18618-689, Botucatu, SP, BrazilUniversidade Estadual PaulistaBotucatuBrazil
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Elías DJ, McMahan CD, Alda F, García-Alzate C, Hart PB, Chakrabarty P. Phylogenomics of trans-Andean tetras of the genus Hyphessobrycon Durbin 1908 (Stethaprioninae: Characidae) and colonization patterns of Middle America. PLoS One 2023; 18:e0279924. [PMID: 36662755 PMCID: PMC9858358 DOI: 10.1371/journal.pone.0279924] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Accepted: 12/16/2022] [Indexed: 01/21/2023] Open
Abstract
Hyphessobrycon is one of the most species rich and widely distributed genera in the family Characidae, with more than 160 species ranging from Veracruz, Mexico to Mar Chiquita Lagoon in Buenos Aires, Argentina. The majority of Hyphessobrycon diversity shows a cis-Andean distribution; only nine species are trans-Andean including H. compressus (Meek 1908). It is well established that Hyphessobrycon is not monophyletic but it has been suggested that natural groups can be identified within the larger Hyphessobrycon species group. In this study, we tested the monophyly of trans-Andean species of Hyphessobrycon and investigated the placement of H. compressus. We inferred the first phylogenomic hypothesis of trans-Andean Hyphessobrycon that includes nearly complete taxonomic sampling (eight of nine valid species) using ultraconserved elements (UCEs). We analyzed 75% (1682 UCEs), 90% (1258 UCEs), and 95% (838 UCEs) complete data matrices, and inferred phylogenomic hypotheses under concatenation and coalescent approaches. In all cases, we recovered the monophyly of trans-Andean Hyphessobrycon inclusive of H. compressus, strong support for three species groups, and evidence of cryptic diversity within the widespread H. compressus and H. condotensis. We used our phylogenomic hypothesis to investigate the biogeographic history of Hyphessobrycon in Middle America. Our ancestral range estimation analysis suggests a single event of cis- to trans-Andean colonization followed by stepwise colonization from the Pacific slope of northwestern South America (Chocó block) to northern Middle America (Maya block). Our work supports the recognition of the trans-Andean species as Hyphessobrycon sensu stricto and provides an evolutionary template to examine morphological characters that will allow us to better understand the diversity of Hyphessobrycon in Middle America.
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Affiliation(s)
- Diego J. Elías
- Museum of Natural Science, Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana, United States of America
- Field Museum of Natural History, Chicago, Illinois, United States of America
| | - Caleb D. McMahan
- Field Museum of Natural History, Chicago, Illinois, United States of America
| | - Fernando Alda
- Department of Biology, Geology and Environmental Science, University of Tennessee at Chattanooga, Chattanooga, Tennessee, United States of America
- SimCenter: Center for Excellence in Applied Computational Science and Engineering, University of Tennessee at Chattanooga, Chattanooga, Tennessee, United States of America
| | - Carlos García-Alzate
- Grupo de Investigación Estudios en Sistemática y Conservación, Universidad del Atlántico-Corporación Universitaria Autónoma del Cauca, Popayán, Colombia
| | - Pamela B. Hart
- Museum of Natural Science, Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana, United States of America
- Department of Biological Sciences, The University of Alabama, Tuscaloosa, AL, United States of America
| | - Prosanta Chakrabarty
- Museum of Natural Science, Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana, United States of America
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Melo BF, de Pinna MCC, Rapp Py-Daniel LH, Zuanon J, Conde-Saldaña CC, Roxo FF, Oliveira C. Paleogene emergence and evolutionary history of the Amazonian fossorial fish genus Tarumania (Teleostei: Tarumaniidae). Front Ecol Evol 2022. [DOI: 10.3389/fevo.2022.924860] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
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.
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