Phylogeny and molecular identification of fishes of the superorder Ostariophysi (Chordata: Actinopterygii) using genomic approaches

• Grant number: 20/13433-6
• Support Opportunities: Research Projects - Thematic Grants
• Start date: October 01, 2021
• End date: September 30, 2026
• Field of knowledge: Biological Sciences - Genetics - Animal Genetics
• Principal Investigator: Claudio de Oliveira
• Grantee: Claudio de Oliveira
• Host Institution: Instituto de Biociências (IBB). Universidade Estadual Paulista (UNESP). Campus de Botucatu. Botucatu , SP, Brazil
• Associated researchers: Bruno Francelino de Melo ; Fábio Fernandes Roxo ; Fausto Foresti ; Gabriel de Souza da Costa e Silva ; Luz Eneida Ochoa Orrego ; Mario Cesar Cardoso de Pinna ; Ricardo Cardoso Benine
• Associated research grant(s): 23/01497-8 - Phylogenetic relation of Stevardiinae with emphasis in Diapomini tribe (Characiformes: Characidae) utilizing the ultra-conserved elements of the genome, AP.R
• Associated scholarship(s): 24/23112-3 - Phylogenetic analysis in Deuterodon and similar genera, as a model of search for evolutionary patterns in monophyletic groups of Characidae (Ostariophysi, Characiformes), BP.PD; 24/22626-3 - Taxonomy, systematics, and museomics of Glanapteryginae and Sarcoglanidinae: Understanding the evolution and diversification of the most aberrant subfamilies in Ostariophysi, BP.PD; 24/22720-0 - Phylogenomics of Myleinae (Characiformes: Serrasalmidae) based on ultraconserved elements (UCEs): exploring evolutionary relationships and diversity, BP.DR; + associated scholarships 24/13929-2 - DESCRIPTION OF A NEW SPECIES OF ARMORED CATFISH OF THE GENUS Loricariichthys (LORICARIIDAE: LORICARIINAE) FROM THE ARAGUAIA RIVER BASIN, BP.IC; 23/12170-0 - Molecular characterization of Chirocentrodon bleekerianus (Clupeiformes: Pristigasteridae), BP.IC; 23/09871-6 - Unraveling the diversity and origins of the genus Characidium (Characiformes: Crenuchidae) in the Neotropical region: a study of Systematics and Biogeography with a genomic and integrative approach, BP.PD; 23/07838-1 - Understanding the Role of Reticulation on the Relationships of Ostariophysan Orders Using Phylogenetic Networks, BP.PD; 23/01862-8 - Phylogenomic of members of the family Aspredinidae (Siluriformes: Ostariophysi), BP.MS; 22/06543-5 - Molecular delimitation of species of the genus Phenacorhamdia Dahl, 1961 (Siluriformes: Heptapteridae), BP.IC; 21/12979-8 - Phylogenetic relationships among genera and families of Siluriformes using ultraconserved elements, BP.PD - associated scholarships

Abstract

Ostariophysi is one of the largest fish superorders, formed almost exclusively by freshwater species, with about 95 families, about 1,500 genera and 11,000 species, thus containing approximately 30% of the known fish species in the world and almost 70 % of freshwater species. Ostariophysi are present all over the world, except in Antarctica, where only fossils are known. Despite the great richness of species and, therefore, their great scientific and economic importance, there are still many problems in the identification of species and in the understanding of the relationships between the internal groups of the superorder (and consequently in their classification), as well as doubts in their processes of diversification and historical biogeography, which need to be addressed with modern and resolving methodologies. To address the issue of molecular identification of all specimens analyzed, we are proposing the sequencing of their complete mitochondrial DNAs, which will allow the creation of a large database, which can be used in the future in many DNA barcode (molecular identification) projects, projects with ecological objectives (environmental DNA), species regulation and control (forensic DNA) and also for the elaboration of mitochondrial phylogenies. To address questions about the relationships between groups (phylogenies) and their processes of diversification (macroevolution) and historical biogeography, markers called ultraconserved elements (UCEs) will be used. The use of this class of genomic molecular markers in studies of phylogeny, macroevolution and historical biogeography has grown considerably in recent years, including several studies published by our research group, confirming the advantages of its use in such a study. For the realization of this project, a large network of collaborators from Brazil and abroad is being assembled, all of them with great experience in the study of fish, which will allow not only the satisfactory realization of this project, but also the realization of numerous future projects. (AU)

Scientific publications

(25)

(References retrieved automatically from Web of Science and SciELO through information on FAPESP grants and their corresponding numbers as mentioned in the publications by the authors)

VILLA-VERDE, LEANDRO; DE PINNA, MARIO C. C.; REIS, VINICIUS J. C.; OYAKAWA, OSVALDO T.. Secretive fish diversity: A new species of Listrura (Siluriformes, Trichomycteridae) from a supposedly well-known river in south-eastern Brazil. Journal of Fish Biology, v. 100, n. 5, p. 12-pg., 2022-04-12. (20/13433-6)

MATTOX, GEORGE M. T.; CETRA, MAURICIO; SOUZA, CAMILA S.; OYAKAWA, OSVALDO T.; BENTO, RODRIGO M. M.; OLIVEIRA, CLAUDIO. Spintherobolus papilliferus in the rio Ribeira de Iguape basin: implications for the biogeography and conservation of an endangered species (Ostariophysi: Characiformes). Neotropical Ichthyology, v. 21, n. 2, p. 19-pg., 2023-01-01. (17/01970-4, 20/13433-6, 17/25860-3)

ADACHI, AISNI M. C. L.; ROQUE, POLLYANA C. G.; HAZIN, FABIO H. V.; VIANNA, MARCELO; ROTUNDO, MATHEUS M.; OLIVEIRA, CLAUDIO; FORESTI, FAUSTO; CRUZ, VANESSA P.. Genetic Population Structure and Diversity of the Whitetail Dogfish Squalus albicaudus (Chondrichthyes, Squaliformes) along the Brazilian Coast as Identified by SNP Markers. FISHES, v. 8, n. 7, p. 11-pg., 2023-07-01. (19/15148-0, 20/13433-6)

REIS, VINICIUS; DE PINNA, MARIO. Diversity and systematics of Trichomycterus Valenciennes 1832 (Siluriformes: Trichomycteridae) in the Rio Doce Basin: iterating DNA, phylogeny and classical taxonomy. ZOOLOGICAL JOURNAL OF THE LINNEAN SOCIETY, v. N/A, p. 98-pg., 2022-06-17. (16/25467-7, 15/26804-4, 20/13433-6)

MARCENIUK, ALEXANDRE PIRES; OLIVEIRA, CLAUDIO; FERRARIS, CARL J.. A new classification of the family Ariidae (Osteichthyes: Ostariophysi: Siluriformes) based on combined analyses of morphological and molecular data. ZOOLOGICAL JOURNAL OF THE LINNEAN SOCIETY, v. N/A, p. 51-pg., 2023-08-21. (16/09204-6, 14/26508-3, 20/13433-6, 18/20610-1)

MELO, BRUNO F.; OTA, RAFAELA P.; BENINE, RICARDO C.; CARVALHO, FERNANDO R.; LIMA, FLAVIO C. T.; MATTOX, GEORGE M. T.; SOUZA, CAMILA S.; FARIA, TIAGO C.; REIA, LAIS; ROXO, FABIO F.; et al. Phylogenomics of Characidae, a hyper-diverse Neotropical freshwater fish lineage, with a phylogenetic classification including four families (Teleostei: Characiformes). ZOOLOGICAL JOURNAL OF THE LINNEAN SOCIETY, v. 202, n. 1, p. 37-pg., 2024-09-03. (17/06551-0, 12/03404-2, 20/13433-6, 11/11422-8, 16/11313-8, 17/01970-4, 21/00242-0, 14/26508-3)

SILVA, GABRIEL S. C.; ROCHA, MARCELO S.; MELO, BRUNO F.; REIA, LAIS; ROXO, FABIO F.; SABAJ, MARK H.; OLIVEIRA, CLAUDIO. Phylogenomics of the catfish family Pimelodidae with focus on the genus Pimelodus support the recognition of Sorubiminae and Pimelodinae (Teleostei, Siluriformes). ZOOLOGICA SCRIPTA, v. 53, n. 5, p. 14-pg., 2024-06-08. (21/12979-8, 20/13433-6, 16/11313-8, 23/09902-9, 22/13025-0, 14/26508-3)

DE OLIVEIRA, RIANNE CAROLINE; BRITZKE, RICARDO; DE OLIVEIRA, CLAUDIO; DA GRACA, WEFERSON JUNIO. Species delimitation in Neotropical fishes of Mesonauta Günther 1862 (Cichliformes: Cichlidae). ORGANISMS DIVERSITY & EVOLUTION, v. N/A, p. 13-pg., 2025-03-25. (20/13433-6)

NIRCHIO, MAURO; OLIVEIRA, CLAUDIO; CIOFFI, MARCELO DE BELLO; SASSI, FRANCISCO M. C.; RIZZI, FRANCISCO PROVENZANO; BENAVIDES, SANTIAGO WLADIMIR NUNEZ; BERRONES, ALISON JAZMIN CALDERON; ROMERO, JUAN FRANCISCO RIVADENEIRA; DEON, GEIZE APARECIDA; KURANAKA, MARIANA; et al. Integrative morphological, cytogenetic and molecular characterization of the Andean climbing catfish Astroblepus mindoensis (Regan, 1916) (Siluriformes:Astroblepidae). Journal of Fish Biology, v. N/A, p. 13-pg., 2024-10-09. (23/08116-0, 20/02681-9, 22/04261-2, 20/13433-6, 23/00955-2)

MATTOX, GEORGE M. T.; LIMA, FLAVIO C. T.; BRITZ, RALF; SOUZA, CAMILA S.; OLIVEIRA, CLAUDIO. Two new miniature species of the fish genus Priocharax from the Rio Tapajos and Amazonas drainages, Para, Brazil (Teleostei: Characiformes: Characidae). VERTEBRATE ZOOLOGY, v. 74, p. 18-pg., 2024-09-12. (17/01970-4, 17/06551-0, 20/13433-6)

ZANATA, ANGELA MARIA; OLIVEIRA, CLAUDIO; OLIVEIRA-SILVA, LEONARDO. Integrative taxonomy reveals a new species of Characidium (Characiformes: Crenuchidae) shared by tributaries of upper Tapajos and Xingu river basins, Brazil. Journal of Fish Biology, v. N/A, p. 10-pg., 2024-09-22. (20/13433-6, 11/50282-7, 23/09871-6)

FLÁVIO C.T. LIMA; CÁRLISON SILVA-OLIVEIRA; CLÁUDIO OLIVEIRA; TIAGO C. FARIA. A new Hyphessobrycon (Characiformes: Acestrorhamphidae) from the Central Amazon basin, Brazil. Papéis Avulsos de Zoologia (São Paulo), v. 65, 2025-03-03. (11/51532-7, 13/20936-0, 21/00242-0, 20/13433-6)

SILVA, GABRIEL DE SOUZA DA COSTA E; SABAJ, MARK HENRY; DE CARVALHO, KAYLANE RODRIGUES; OLIVEIRA, CLAUDIO. Integrative Taxonomy Reveals a New Species of Imparfinis (Siluriformes: Heptapteridae) from the Upper Xingu River Basin. ICHTHYOLOGY AND HERPETOLOGY, v. 113, n. 1, p. 11-pg., 2025-04-01. (21/12979-8, 20/13433-6, 22/13025-0)

DIAS, ANGELICA C.; TENCATT, LUIZ F. C.; ROXO, FABIO F.; SILVA, GABRIEL DE SOUZA DA COSTA; SANTOS, SERGIO A.; BRITTO, MARCELO R.; TAYLOR, MARTIN, I; OLIVEIRA, CLAUDIO. Phylogenomic analyses in the complex Neotropical subfamily Corydoradinae (Siluriformes: Callichthyidae) with a new classification based on morphological and molecular data. ZOOLOGICAL JOURNAL OF THE LINNEAN SOCIETY, v. N/A, p. 31-pg., 2024-06-11. (20/13433-6)

DE ALMEIDA, RAFAEL B.; AZAMBUJA, MATHEUS; NOGAROTO, VIVIANE; OLIVEIRA, CLAUDIO; ROXO, FABIO F.; ZAWADZKI, CLAUDIO H.; VICARI, MARCELO R.. DNA barcode shows discordant cases among morphological and molecular species identification in Isbrueckerichthys (Siluriformes: Loricariidae). Neotropical Ichthyology, v. 22, n. 3, p. 16-pg., 2024-01-01. (20/13433-6)

VIDAL, MATEUS ROSSETTO; LASMAR, LUCAS F.; NADAI, PAMELA C. F.; OLIVEIRA, CLAUDIO; SILVA, DUILIO M. Z. A.; FORESTI, FAUSTO. Selecting reference genes for RT-qPCR studies involving the presence of B chromosomes in Psalidodon (Characiformes, Characidae). MOLECULAR BIOLOGY REPORTS, v. 51, n. 1, p. 7-pg., 2024-12-01. (17/22447-8, 20/13433-6, 19/15140-9, 20/01775-0)

MELO, BRUNO F.; CONDE-SALDANA, CRISTHIAN C.; VILLA-NAVARRO, FRANCISCO A.; MCMAHAN, CALEB D.; OLIVEIRA, CLAUDIO. Phylogeographic patterns of Cyphocharax from trans-Andean rivers and northward expansion to lower Central America (Teleostei, Curimatidae). Journal of Fish Biology, v. 105, n. 1, p. 12-pg., 2024-05-16. (18/24040-5, 20/13433-6, 18/09767-6)

OLIVEIRA, CLAUDIO; CAIXETA, HELOISA DE CIA; DE MELO, MARCELO ROBERTO SOUTO. The complete mitogenome of Argentina brasiliensis Kobyliansky, 2004 and a phylogenetic analyses of the order Argentiniformes. GENETICS AND MOLECULAR BIOLOGY, v. 47, n. 4, p. 4-pg., 2024-01-01. (17/12909-4, 20/13433-6, 21/05619-5)

STIASSNY, MELANIE L. J.; KEANE, COOPER; MBIMBI, JOSE J. M. M.; MELO, BRUNO F.. Phylogenomics and Morphology of the African Fish Genus Brycinus with Revalidation of Brachyalestes and Description of a New Species from the Congo Basin (Teleostei: Alestidae). ICHTHYOLOGY AND HERPETOLOGY, v. 111, n. 4, p. 15-pg., 2023-12-01. (20/13433-6)

CRISPIM-RODRIGUES, JEFFERSON LUAN; DA COSTA E SILVA, GABRIEL DE SOUZA; SHIBATTA, OSCAR AKIO; KURANAKA, MARIANA; OLIVEIRA, CLAUDIO. Description and phylogenetic position of a new species of Rhyacoglanis (Siluriformes: Pseudopimelodidae) from the Jamanxim River basin. Neotropical Ichthyology, v. 21, n. 3, p. 15-pg., 2023-01-01. (20/13433-6, 22/13025-0, 21/12979-8)

MARCENIUK, ALEXANDRE PIRES; CAIRES, RODRIGO ANTUNES; ROTUNDO, MATHEUS MARCOS; GASPARINI, JOAO LUIZ; BRITO, GITA JUAN SOTERORUDA; CASTILHO, JULIA CRISTINA; CERQUEIRA, NAJILA NOLIE CATARINE DANTAS; OLIVEIRA, CLAUDIO; ESPINDOLA, VINICIUS CORREA. Review of the grunt genus Rhonciscus (Lutjaniformes: Haemulidae) from the Western Atlantic, with the description of a new species from Brazil. MARINE BIODIVERSITY, v. 54, n. 6, p. 19-pg., 2024-12-01. (22/14954-5, 20/13433-6)

DELPIANI, G.; ANTONI, M. Y. DELI; COVATTI, M.; FISCHER, L.; DE ASTARLOA, J. M. DIAZ; OLIVERA, C.; DELPIANI, S. M.. The deception in the identity of the fish bought in some of the biggest cities of Argentina. FOOD CONTROL, v. 163, p. 8-pg., 2024-04-11. (20/13433-6)

TURSELLINO, MAURO NIRCHIO; CIOFFI, MARCELO DE BELLO; SASSI, FRANCISCO DE MENEZES CAVALCANTE; DEON, GEIZE APARECIDA; OLIVEIRA, CLAUDIO; KURANAKA, MARIANA; VALDIVIEZO-RIVERA, JONATHAN; GONZALEZ, VICTOR HUGO; ROSSI, ANNA RITA. Integrating Genomic and Chromosomal Data: A Cytogenetic Study of Transancistrus santarosensis (Loricariidae: Hypostominae) with Characterization of a ZZ/ZW Sex Chromosome System. GENES, v. 14, n. 9, p. 15-pg., 2023-09-01. (20/13433-6)

SILVA, GUILHERME JOS DA COSTA; DA COSTA E SILVA, GABRIEL DE SOUZA; OLIVEIRA, CLAUDIO. A new species of spiny Rineloricaria (Siluriformes: Loricariidae) from the Rio Paraiba do Sul basin and costal rivers from Rio de Janeiro State. Zootaxa, v. 5175, n. 2, p. 8-pg., 2022-08-16. (16/09204-6, 21/12979-8, 18/20610-1, 20/13433-6, 14/26508-3)

MATTOX, GEORGE M. T.; BRITZ, RALF; SOUZA, CAMILA S.; CASAS, ANDRE L. S.; LIMA, FLAVIO C. T.; OLIVEIRA, CLAUDIO. Two new species of miniature tetras of the fish genus Priocharax from the Rio Juru? drainage, Acre, Brazil (Teleostei: Characiformes: Characidae). CANADIAN JOURNAL OF ZOOLOGY, v. N/A, p. 19-pg., 2023-02-10. (17/01970-4, 13/20936-0, 11/51532-7, 20/13433-6)