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Ovchinnikova TV, Shi Q. Editorial: Aquatic genomics and transcriptomics for evolutionary biology. Front Genet 2023; 14:1183637. [PMID: 37214421 PMCID: PMC10196625 DOI: 10.3389/fgene.2023.1183637] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Accepted: 04/19/2023] [Indexed: 05/24/2023] Open
Affiliation(s)
- Tatiana V. Ovchinnikova
- M.M. Shemyakin and Yu.A. Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
- Department of Bioorganic Chemistry, Faculty of Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Qiong Shi
- Shenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, BGI Academy of Marine Sciences, Shenzhen, China
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2
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Yepes-Blandón JA, Bian C, Benítez-Galeano MJ, Aristizabal-Regino JL, Estrada-Posada AL, Mir D, Vásquez-Machado G, Atencio-García VJ, Shi Q, Rodríguez-Osorio N. Draft genome assembly for the colombian freshwater bocachico fish, Prochilodus magdalenae. Front Genet 2023; 13:989788. [PMID: 36744175 PMCID: PMC9893009 DOI: 10.3389/fgene.2022.989788] [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: 07/08/2022] [Accepted: 12/13/2022] [Indexed: 01/21/2023] Open
Abstract
We report the first draft genome assembly for Prochilodus magdalenae, the leading representative species of the Prochilodontidae family in Colombia. This 1.2-Gb assembly, with a GC content of 42.0% and a repetitive content of around 31.0%, is in the range of previously reported characid species genomes. Annotation identified 34,725 nuclear genes, and BUSCO completeness value was 94.9%. Gene ontology and primary metabolic pathway annotations indicate similar gene profiles for P. magdalenae and the closest species with annotated genomes: blind cave fish (Astyanax mexicanus) and red piranha (Pygocentrus nattereri). A comparative analysis showed similar genome traits to other characid species. The fully sequenced and annotated mitochondrial genome reproduces the taxonomic classification of P. magdalenae and confirms the low mitochondrial genetic divergence inside the Prochilodus genus. Phylogenomic analysis, using nuclear single-copy orthologous genes, also confirmed the evolutionary position of the species. This genome assembly provides a high-resolution genetic resource for sustainable P. magdalenae management in Colombia and, as the first genome assembly for the Prochilodontidae family, will contribute to fish genomics throughout South America.
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Affiliation(s)
| | - Chao Bian
- Shenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, BGI Academy of Marine Sciences, BGI Marine, Shenzhen, Guangdong, China
| | - María José Benítez-Galeano
- Unidad de Genómica y Bioinformática, Departamento de Ciencias Biológicas, CENUR Litoral Norte, Universidad de la República, Salto, Uruguay
| | | | | | - Daiana Mir
- Unidad de Genómica y Bioinformática, Departamento de Ciencias Biológicas, CENUR Litoral Norte, Universidad de la República, Salto, Uruguay
| | | | | | - Qiong Shi
- Shenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, BGI Academy of Marine Sciences, BGI Marine, Shenzhen, Guangdong, China
| | - Nélida Rodríguez-Osorio
- Unidad de Genómica y Bioinformática, Departamento de Ciencias Biológicas, CENUR Litoral Norte, Universidad de la República, Salto, Uruguay
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3
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Taphorn DC, Liverpool E, Lujan NK, DoNascimiento C, Hemraj DD, Crampton WGR, Kolmann MA, Fontenelle JP, de Souza LS, Werneke DC, Ram M, Bloom DD, Sidlauskas BL, Holm E, Lundberg JG, Sabaj MH, Bernard C, Armbruster JW, López-Fernández H. Annotated checklist of the primarily freshwater fishes of Guyana. PROCEEDINGS OF THE ACADEMY OF NATURAL SCIENCES OF PHILADELPHIA 2022. [DOI: 10.1635/053.168.0101] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
| | - Elford Liverpool
- Department of Biology, Faculty of Natural Sciences, University of Guyana, Turkeyen, East Coast Demerara, 413741, Georgetown, Guyana.
| | - Nathan K. Lujan
- Department of Natural History, Royal Ontario Museum, 100 Queen's Park, Toronto, Ontario, M5S 2C6, Canada and Department of Ecology and Evolutionary Biology, University of Toronto, 25 Willcocks Street, Toronto, Ontario, M5S 3B2, Canada
| | - Carlos DoNascimiento
- Universidad de Antioquia, Grupo de Ictiología, Instituto de Biología, Calle 67 No. 53-108, Medellín, Antioquia, Colombia
| | - Devya D. Hemraj
- Centre for the Study of Biological Diversity, Department of Biology, Faculty of Natural Sciences, University of Guyana, Turkeyen Campus, Greater Georgetown, Guyana
| | | | - Matthew A. Kolmann
- Department of Biology, University of Louisville, Louisville, KY, 40292, USA
| | - João Pedro Fontenelle
- University of Toronto, Institute of Forestry and Conservation, 33 Willcocks St. Office 4004, M5S 3E8, Toronto, ON, Canada
| | - Lesley S. de Souza
- Field Museum of Natural History, 1400 S. Lake Shore, Chicago, IL, 60605 USA
| | - David C. Werneke
- Department of Biological Sciences, 101 Rouse, Auburn University, Auburn, AL, 36849, USA
| | - Mark Ram
- Department of Biology, Faculty of Natural Sciences, University of Guyana, Turkeyen Campus, Greater Georgetown, Guyana
| | - Devin D. Bloom
- Department of Biological Sciences and Institute of the Environment & Sustainability, Western Michigan University, Kalamazoo, MI, 49008-5410, USA
| | - Brian L. Sidlauskas
- Oregon State University, Department of Fisheries, Wildlife and Conservation Sciences, 104 Nash Hall, Corvallis, Oregon, 97331-3803 USA and Department of Vertebrate Zoology, National Museum of Natural History, Smithsonian Institution, Washington, Dist
| | - Erling Holm
- Department of Natural History, Royal Ontario Museum, 100 Queen's Park, Toronto, Ontario, M5S 2C6, Canada
| | - John G. Lundberg
- The Academy of Natural Sciences of Drexel University, 1900 Benjamin Franklin Parkway, Philadelphia, PA, 19103, USA
| | - Mark H. Sabaj
- The Academy of Natural Sciences of Drexel University, 1900 Benjamin Franklin Parkway, Philadelphia, PA, 19103, USA
| | - Calvin Bernard
- Department of Biology, Faculty of Natural Sciences, University of Guyana, Turkeyen Campus, Greater Georgetown, Guyana
| | | | - Hernán López-Fernández
- Department of Ecology and Evolutionary Biology and Museum of Zoology, University of Michigan, 1105 North University Ave. Ann Arbor, MI, 48109, USA
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4
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Frable BW, Melo BF, Fontenelle JP, Oliveira C, Sidlauskas BL. Biogeographic reconstruction of the migratory Neotropical fish family Prochilodontidae (Teleostei: Characiformes). ZOOL SCR 2022. [DOI: 10.1111/zsc.12531] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Affiliation(s)
- Benjamin W. Frable
- Marine Vertebrate Collection Scripps Institution of Oceanography University of California San Diego La Jolla California USA
| | - Bruno F. Melo
- Department of Ichthyology American Museum of Natural History New York New York USA
| | - João P. Fontenelle
- Institute of Forestry and Conservation University of Toronto Toronto Ontario Canada
| | - Claudio Oliveira
- Departamento de Biologia Estrutural e Funcional, Instituto de Biociências Universidade Estadual Paulista Botucatu São Paulo Brazil
| | - Brian L. Sidlauskas
- Department of Fisheries, Wildlife and Conservation Sciences Oregon State University Corvallis Oregon USA
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5
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Two novel species of Myxobolus parasitizing the gills of Semaprochilodus insignis in the Brazilian Amazon. Microb Pathog 2022; 165:105464. [PMID: 35247498 DOI: 10.1016/j.micpath.2022.105464] [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: 07/30/2021] [Revised: 02/18/2022] [Accepted: 02/28/2022] [Indexed: 11/23/2022]
Abstract
The present study describes two new Myxobolus species infecting the gills of Semaprochilodus insignis, the most consumed freshwater fish species in the Brazilian Amazon. The fish specimens were caught in the Tapajós River, in the state of Pará, and the morphological, ultrastructural, small subunit ribosomal DNA (ssrDNA), and phylogenetic data of the myxosporean species were obtained. Two species of Myxobolus were found in the gills of S. insignis. Myxobolus maiai n. sp. developed in the gill filaments, and mature myxospores were round-shaped from the frontal view, measuring 12.5-14.8 (13.9 ± 0.5) μm in length, 11.4-13.8 (12.3 ± 0.5) μm in width, and have a thickness of 6.4-7.7 (6.9 ± 0.6) μm in the lateral view, with symmetric values. Its polar capsules were 4.4-6.6 (5.5 ± 0.5) μm in length and 2.3-3.7 (3.0 ± 0.3) μm in width, and the polar tubules had 4 - 5 coils. Myxobolus iarakiensis n. sp. was found infecting the gill arch. Mature myxospores were oval-shaped from the frontal view, and measured 6.7-8.6 (8.0 ± 0.4) μm in length, 4.5-6.3 (5.6 ± 0.4) μm in width, and had a thickness of 2.7-4.7 (3.8 ± 0.5) μm in the lateral view, with symmetric values. Its polar capsules were 2.1-3.7 (2.9 ± 0.3) μm in length and 1.1-2.0 (1.5 ± 0.2) μm in width, and its polar tubules had 4 - 5 coils. The ssrDNA based phylogeny showed these two novel species as grouping in a clade composed of parasite species of Prochilodontidae hosts.
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Ribolli J, Zaniboni Filho E, Scaranto BMS, Shibatta OA, Machado CB. Cryptic diversity and diversification processes in three cis-Andean Rhamdia species (Siluriformes: Heptapteridae) revealed by DNA barcoding. Genet Mol Biol 2021; 44:e20200470. [PMID: 34254973 PMCID: PMC8276235 DOI: 10.1590/1678-4685-gmb-2020-0470] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Accepted: 04/07/2021] [Indexed: 12/02/2022] Open
Abstract
The wide distribution of the Neotropical freshwater catfish Rhamdia offers an excellent opportunity to investigate the historical processes responsible for modeling South America’s hydrogeological structure. We used sequences from cis-Andean and Mesoamerican Rhamdia species to reconstruct and estimate divergence times among cis-Andean lineages, correlating the results with known geological events. Species delimitation methods based on distance (DNA barcoding and BIN) and coalescence (GMYC) approaches identified nine well-supported lineages from the cis-Andean region from sequences available in the BOLD dataset. The cis-Andean Rhamdia lineages diversification process began in Eocene and represented the split between cis-Andean and Mesoamerican clades. The cis-Andean clade contains two principal groups: Northwest clade (MOTUs from Amazon, Essequibo, Paraguay, and Itapecuru basins) and Southeast clade (Eastern Brazilian shield basins (Paraná, Uruguay, Iguaçu, and São Francisco) plus eastern coastal basins). The diversification of the cis-Andean Rhamdia lineages results from vicariance and geodispersion events, which played a key role in the current intricate distribution pattern of the Rhamdia lineages. The wide geographical distribution and large size of the specimens make it attractive to cultivate in different countries of the Neotropical region. The lineages delimitation minimizes identification mistakes, unintentional crossings by aquaculture, and reduces natural stocks contamination.
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Affiliation(s)
- Josiane Ribolli
- Universidade Federal de Santa Catarina, Departamento de Aquicultura, Lagoa do Peri, Laboratório de Biologia e Cultivo de Peixes de Água Doce, Florianópolis, SC, Brazil
| | - Evoy Zaniboni Filho
- Universidade Federal de Santa Catarina, Departamento de Aquicultura, Lagoa do Peri, Laboratório de Biologia e Cultivo de Peixes de Água Doce, Florianópolis, SC, Brazil
| | - Bianca Maria Soares Scaranto
- Universidade Federal de Santa Catarina, Departamento de Aquicultura, Lagoa do Peri, Laboratório de Biologia e Cultivo de Peixes de Água Doce, Florianópolis, SC, Brazil
| | - Oscar Akio Shibatta
- Universidade Estadual de Londrina, Departamento de Biologia Animal e Vegetal, Centro de Ciências Biológicas, Londrina, PR, Brazil
| | - Carolina Barros Machado
- Universidade Federal de São Carlos, Departamento de Genética e Evolução, São Carlos, SP, Brazil
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7
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Melo BF, Sidlauskas BL, Near TJ, Roxo FF, Ghezelayagh A, Ochoa LE, Stiassny MLJ, Arroyave J, Chang J, Faircloth BC, MacGuigan DJ, Harrington RC, Benine RC, Burns MD, Hoekzema K, Sanches NC, Maldonado-Ocampo JA, Castro RMC, Foresti F, Alfaro ME, Oliveira C. Accelerated Diversification Explains the Exceptional Species Richness of Tropical Characoid Fishes. Syst Biol 2021; 71:78-92. [PMID: 34097063 DOI: 10.1093/sysbio/syab040] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2021] [Revised: 06/01/2021] [Accepted: 06/04/2021] [Indexed: 11/12/2022] Open
Abstract
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.
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Affiliation(s)
- Bruno F Melo
- Dept of Structural and Functional Biology, Institute of Biosciences, São Paulo State University, Botucatu, SP, 16818-689, Brazil
| | - Brian L Sidlauskas
- Dept of Fisheries and Wildlife, Oregon State University, Corvallis, OR, 97331, USA
| | - Thomas J Near
- Dept of Ecology and Evolutionary Biology, Yale University, New Haven, CT, 06520, USA
| | - Fabio F Roxo
- Sector of Zoology, Institute of Biosciences, São Paulo State University, Botucatu, SP, 18618-689, Brazil
| | - Ava Ghezelayagh
- Dept of Ecology and Evolutionary Biology, Yale University, New Haven, CT, 06520, USA
| | - Luz E Ochoa
- Dept of Structural and Functional Biology, Institute of Biosciences, São Paulo State University, Botucatu, SP, 16818-689, Brazil.,Instituto de Investigación de Recursos Biológicos Alexander von Humboldt, Palmira, Valle del Cauca, 763547, Colombia
| | - Melanie L J Stiassny
- Dept of Ichthyology, American Museum of Natural History, New York, NY, 10024, USA
| | - Jairo Arroyave
- Instituto de Biología, Universidad Nacional Autónoma de México, Ciudad de México, 04510, México
| | - Jonathan Chang
- School of Biological Sciences, Monash University, Melbourne, VIC, 3800, Australia
| | - Brant C Faircloth
- Dept of Biological Sciences and Museum of Natural Science, Louisiana State University, Baton Rouge, LA, 70803, USA
| | - Daniel J MacGuigan
- Dept of Ecology and Evolutionary Biology, Yale University, New Haven, CT, 06520, USA
| | - Richard C Harrington
- Dept of Ecology and Evolutionary Biology, Yale University, New Haven, CT, 06520, USA
| | - Ricardo C Benine
- Sector of Zoology, Institute of Biosciences, São Paulo State University, Botucatu, SP, 18618-689, Brazil
| | - Michael D Burns
- Cornell Lab of Ornithology, Cornell University Museum of Vertebrates, Ithaca, NY, 14850, USA
| | - Kendra Hoekzema
- Dept of Fisheries and Wildlife, Oregon State University, Corvallis, OR, 97331, USA
| | - Natalia C Sanches
- Dept of Structural and Functional Biology, Institute of Biosciences, São Paulo State University, Botucatu, SP, 16818-689, Brazil
| | - Javier A Maldonado-Ocampo
- Dept de Biología, Facultad de Ciencias, Pontificia Universidad Javeriana, Bogotá, DC, Colombia (in memoriam)
| | - Ricardo M C Castro
- Faculdade de Filosofia, Ciências e Letras, Universidade de São Paulo, Ribeirão Preto, SP, 14040-901, Brazil
| | - Fausto Foresti
- Dept of Structural and Functional Biology, Institute of Biosciences, São Paulo State University, Botucatu, SP, 16818-689, Brazil
| | - Michael E Alfaro
- Dept of Ecology and Evolutionary Biology, University of California, Los Angeles, CA, 90095, USA
| | - Claudio Oliveira
- Dept of Structural and Functional Biology, Institute of Biosciences, São Paulo State University, Botucatu, SP, 16818-689, Brazil
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Santos RP, Melo BF, Yazbeck GM, Oliveira RS, Hilário HO, Prosdocimi F, Carvalho DC. Diversification of
Prochilodus
in the eastern Brazilian Shield: Evidence from complete mitochondrial genomes (Teleostei, Prochilodontidae). J ZOOL SYST EVOL RES 2021. [DOI: 10.1111/jzs.12475] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Affiliation(s)
- Rosiane P. Santos
- Laboratório de Genética da Conservação Programa de Pós‐Graduação em Biologia dos Vertebrados Pontifícia Universidade Católica de Minas Gerais Belo Horizonte Brazil
- Laboratório de Recursos Genéticos Programa de Pós‐Graduação em Ecologia Universidade Federal de São João del‐Rei São João del‐Rei Brazil
| | - Bruno F. Melo
- Departamento de Biologia Estrutural e Funcional Instituto de Biociências Universidade Estadual Paulista Botucatu Brazil
| | - Gabriel M. Yazbeck
- Laboratório de Recursos Genéticos Programa de Pós‐Graduação em Ecologia Universidade Federal de São João del‐Rei São João del‐Rei Brazil
| | - Rafael S. Oliveira
- Programa de Pós‐Graduação em Ciência da Computação Universidade Federal de São João del‐Rei São João del‐Rei Brazil
| | - Heron O. Hilário
- Laboratório de Genética da Conservação Programa de Pós‐Graduação em Biologia dos Vertebrados Pontifícia Universidade Católica de Minas Gerais Belo Horizonte Brazil
| | - Francisco Prosdocimi
- Laboratório de Genômica e Biodiversidade Instituto de Bioquímica Médica Leopoldo de MeisUniversidade Federal do Rio de Janeiro Rio de Janeiro Brazil
| | - Daniel C. Carvalho
- Laboratório de Genética da Conservação Programa de Pós‐Graduação em Biologia dos Vertebrados Pontifícia Universidade Católica de Minas Gerais Belo Horizonte Brazil
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9
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Souza CS, Silva GSC, Ochoa LE, Roxo FF, Costa-Silva GJ, Foresti F, Melo BF, Oliveira C. Molecular and morphological diversity in species of Kronichthys (Teleostei, Loricariidae) from Atlantic coastal rivers of Brazil. JOURNAL OF FISH BIOLOGY 2021; 98:668-679. [PMID: 33128401 DOI: 10.1111/jfb.14607] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Revised: 10/23/2020] [Accepted: 10/29/2020] [Indexed: 06/11/2023]
Abstract
The Neotropical catfish genus Kronichthys contains three species distributed along coastal rivers of southern and southeastern Brazil. Although phylogenetic hypotheses are available, the molecular and morphological diversity and species boundaries within the genus remain unexplored. In this study, the authors generated mitochondrial data for 90 specimens combined with morphometric and meristic data to investigate species diversity, species boundaries and putative morphological signatures in Kronichthys. Phylogenetic and species delimitation results clearly show the presence of four genetic lineages, three within Kronichthys heylandi along the coast from Rio de Janeiro to southern São Paulo and a single lineage encompassing both the nominal species Kronichthys lacerta and Kronichthys subteres from the Ribeira de Iguape basin to Santa Catarina in southern Brazil. Nonetheless, morphological data show overlapped ranges in morphometrics and a definition of only two morphotypes, with clear phenotypic differences in the teeth number: K. heylandi differs from K. subteres + K. lacerta by the higher number of premaxillary teeth (30-52 vs. 19-28) and higher number of dentary teeth (28-54 vs. 17-28). Headwater captures and connections of paleodrainages because of sea-level fluctuations represent the two major biogeographic processes promoting species diversification and lineage dispersal of Kronichthys in the Atlantic coastal range of Brazil.
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Affiliation(s)
- Camila S Souza
- Departamento de Biologia Estrutural e Funcional, Instituto de Biociências, Universidade Estadual Paulista, Botucatu, Brazil
| | - Gabriel S C Silva
- Departamento de Bioestatística, Biologia Vegetal, Parasitologia e Zoologia, Instituto de Biociências, Universidade Estadual Paulista, Botucatu, Brazil
| | - Luz E Ochoa
- Museu de Zoologia, Universidade de São Paulo, São Paulo, Brazil
| | - Fabio F Roxo
- Departamento de Bioestatística, Biologia Vegetal, Parasitologia e Zoologia, Instituto de Biociências, Universidade Estadual Paulista, Botucatu, Brazil
| | | | - Fausto Foresti
- Departamento de Biologia Estrutural e Funcional, Instituto de Biociências, Universidade Estadual Paulista, Botucatu, Brazil
| | - Bruno F Melo
- Departamento de Biologia Estrutural e Funcional, Instituto de Biociências, Universidade Estadual Paulista, Botucatu, Brazil
| | - Claudio Oliveira
- Departamento de Biologia Estrutural e Funcional, Instituto de Biociências, Universidade Estadual Paulista, Botucatu, Brazil
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10
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Miranda-Chumacero G, Mariac C, Duponchelle F, Painter L, Wallace R, Cochonneau G, Molina-Rodriguez J, Garcia-Davila C, Renno JF. Threatened fish spawning area revealed by specific metabarcoding identification of eggs and larvae in the Beni River, upper Amazon. Glob Ecol Conserv 2020. [DOI: 10.1016/j.gecco.2020.e01309] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
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11
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Landínez-García RM, Narváez JC, Márquez EJ. Population genetics of the freshwater fish Prochilodus magdalenae (Characiformes: Prochilodontidae), using species-specific microsatellite loci. PeerJ 2020; 8:e10327. [PMID: 33240645 PMCID: PMC7666565 DOI: 10.7717/peerj.10327] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2018] [Accepted: 10/19/2020] [Indexed: 11/29/2022] Open
Abstract
Prochilodus magdalenae is a freshwater fish endemic to the Colombian Magdalena-Cauca and Caribbean hydrographic basins. The genetic structure patterns of populations of different members of Prochilodus and the historic restocking of its depleted natural populations suggest that P. magdalenae exhibits genetic stocks that coexist and co-migrate throughout the rivers Magdalena, Cauca, Cesar, Sinú and Atrato. To test this hypothesis and explore the levels of genetic diversity and population demography of 725 samples of P. magdalenae from the studied rivers, we developed a set of 11 species-specific microsatellite loci using next-generation sequencing, bioinformatics, and experimental tests of the levels of diversity of the microsatellite loci. The results evidenced that P. magdalenae exhibits high genetic diversity, significant inbreeding coefficient ranging from 0.162 to 0.202, and signs of erosion of the genetic pool. Additionally, the population genetic structure constitutes a mixture of genetic stocks heterogeneously distributed along the studied rivers, and moreover, a highly divergent genetic stock was detected in Chucurí, Puerto Berrío and Palagua that may result from restocking practices. This study provides molecular tools and a wide framework regarding the genetic diversity and structure of P. magdalenae, which is crucial to complement its baseline information, diagnosis and monitoring of populations, and to support the implementation of adequate regulation, management, and conservation policies.
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Affiliation(s)
- Ricardo M Landínez-García
- Facultad de Ciencias, Escuela de Biociencias, Laboratorio de Biología Molecular y Celular, Universidad Nacional de Colombia-Sede Medellín, Medellín, Colombia
| | - Juan Carlos Narváez
- Grupo de Biodiversidad y Ecología Aplicada, Laboratorio de Genética Molecular, Universidad del Magdalena, Santa Marta, Magdalena, Colombia
| | - Edna J Márquez
- Facultad de Ciencias, Escuela de Biociencias, Laboratorio de Biología Molecular y Celular, Universidad Nacional de Colombia-Sede Medellín, Medellín, Colombia
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12
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Hidden diversity in Prochilodus nigricans: A new genetic lineage within the Tapajós River basin. PLoS One 2020; 15:e0237916. [PMID: 32842138 PMCID: PMC7447553 DOI: 10.1371/journal.pone.0237916] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2020] [Accepted: 08/06/2020] [Indexed: 11/23/2022] Open
Abstract
Highly spread through the Amazon River basin, Prochilodus nigricans have had its taxonomic validity recently questioned, when genetic differences between Western and Eastern Amazon populations from the Brazilian shield were detected. This area has been seeing as a region of high ichthyofaunal diversity and endemism, in which the hybrid origin of the Tapajós River basin has been raised. In this paper, we report a new molecular lineage within P. nigricans of Tapajós River, highlighting this region still hides taxonomically significant diversity. Haplotype networks were reconstructed using the mitochondrial COI and ATP6/8 markers, which were also used to calculate genetic distances among clusters. We additionally conducted a delimiting species approach by employing a Generalized Mixed Yule-Coalescent model (GMYC) with COI sequences produced here, and previous ones published for individuals sampled across the Amazon River basin. In addition to the genetic differentiation within P. nigricans, our findings favor the hypothesis of hybrid origin of the Tapajós River basin and reaffirm the importance of studies aiming to investigate hidden diversity to address taxonomic and biogeographic issues, that certainly benefit better biodiversity conservation actions.
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13
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Chagas ATDA, Ludwig S, Pimentel JDSM, de Abreu NL, Nunez-Rodriguez DL, Leal HG, Kalapothakis E. Use of complete mitochondrial genome sequences to identify barcoding markers for groups with low genetic distance. Mitochondrial DNA A DNA Mapp Seq Anal 2020; 31:139-146. [PMID: 32314625 DOI: 10.1080/24701394.2020.1748609] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
Complete mitochondrial sequences can be rapidly obtained and are widely available, providing a great source of species information and allowing for the discovery of new specific molecular markers. However, for some taxonomic groups, traditional approaches for species delimitation are impaired by the low genetic distance values. In these cases, other species-level markers are used. For Prochilodus, which includes important neotropical fish species, species-level delimitation usually results in poor phylogenetic resolution when using mitochondrial COI/cytB genes as barcoding markers because of low genetic variability and low species-level resolution. Thus, in this study, we developed an approach to design and validate new barcoding markers with high species-level resolution obtained from the D-loop region, using Prochilodus spp. as a model. For the new barcoding marker validation, the amplicon region was used to infer the phylogenetic relationships of Prochilodus spp. through three distinct methods: Bayesian inference (BI), Neighbor-Joining method (NJ), and Maximum Likelihood method (ML). The phylogenetic relationships of Prochilodus spp. revealed high resolution at species-level, nonoverlapping clades, and high branch support. The genetic distance results allied to two different clustering methods (Bayesian Poisson tree processes and automatic barcode gap discovery) revealed the existence of a barcoding gap, thus, validating the use of the barcoding markers designed in this study. The approach proposed here may, therefore, be expanded to other taxa to access and validate new barcoding markers with higher resolution at the species level.
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Affiliation(s)
- Aline Torres de Azevedo Chagas
- Department of Genetics, Ecology and Evolution, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, Brazil
| | - Sandra Ludwig
- Department of Genetics, Ecology and Evolution, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, Brazil
| | - Juliana da Silva Martins Pimentel
- Department of Genetics, Ecology and Evolution, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, Brazil.,Pitágoras College, Belo Horizonte, Brazil
| | - Nazaré Lúcio de Abreu
- Department of Genetics, Ecology and Evolution, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, Brazil
| | - Daniela Lidia Nunez-Rodriguez
- Department of Genetics, Ecology and Evolution, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, Brazil
| | - Hortensia Gomes Leal
- Department of Genetics, Ecology and Evolution, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, Brazil
| | - Evanguedes Kalapothakis
- Department of Genetics, Ecology and Evolution, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, Brazil
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14
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Faircloth BC, Alda F, Hoekzema K, Burns MD, Oliveira C, Albert JS, Melo BF, Ochoa LE, Roxo FF, Chakrabarty P, Sidlauskas BL, Alfaro ME. A Target Enrichment Bait Set for Studying Relationships among Ostariophysan Fishes. COPEIA 2020. [DOI: 10.1643/cg-18-139] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Affiliation(s)
- Brant C. Faircloth
- Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana 70803; (BCF) ; and (PC) . Send reprint requests to BCF
| | - Fernando Alda
- Department of Biology, Geology and Environmental Science, University of Tennessee at Chattanooga, Chattanooga, Tennessee 37403;
| | - Kendra Hoekzema
- Department of Fisheries and Wildlife, Oregon State University, Corvallis, Oregon 97331; (KH) ; and (BLS)
| | - Michael D. Burns
- Department of Fisheries and Wildlife, Oregon State University, Corvallis, Oregon 97331; (KH) ; and (BLS)
| | - Claudio Oliveira
- Departamento de Morfologia, Instituto de Biociências, Universidade Estadual Paulista, Botucatu, São Paulo 18618-689, Brazil; (CO) ; (BFM) ; and (LEO)
| | - James S. Albert
- Department of Biology, University of Louisiana at Lafayette, Lafayette, Louisiana 70503;
| | - Bruno F. Melo
- Departamento de Morfologia, Instituto de Biociências, Universidade Estadual Paulista, Botucatu, São Paulo 18618-689, Brazil; (CO) ; (BFM) ; and (LEO)
| | - Luz E. Ochoa
- Departamento de Morfologia, Instituto de Biociências, Universidade Estadual Paulista, Botucatu, São Paulo 18618-689, Brazil; (CO) ; (BFM) ; and (LEO)
| | - Fábio F. Roxo
- Departamento de Zoologia, Instituto de Biociências, Universidade Estadual Paulista, Botucatu, SP, Brazil;
| | - Prosanta Chakrabarty
- Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana 70803; (BCF) ; and (PC) . Send reprint requests to BCF
| | - Brian L. Sidlauskas
- Department of Fisheries and Wildlife, Oregon State University, Corvallis, Oregon 97331; (KH) ; and (BLS)
| | - Michael E. Alfaro
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, California 90095;
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15
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Guimarães EC, Silva de Brito P, Feitosa LM, Carvalho Costa L, Ottoni FP. A new cryptic species of Hyphessobrycon Durbin, 1908 (Characiformes, Characidae) from the Eastern Amazon, revealed by integrative taxonomy. ZOOSYST EVOL 2019. [DOI: 10.3897/zse.95.34069] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Hyphessobryconcarusp. nov. is described based on five different and independent methods of species delimitation, making the hypothesis of this new species supported by an integrative taxonomy perspective. This new species has a restricted distribution, occurring just in the upper Pindaré river drainage, Mearim river basin, Brazil. It is a member of the rosy tetra clade, which is characterized mainly by the presence of a dark brown or black blotch on dorsal fin and absence of a midlateral stripe on the body. Hyphessobryconcarusp. nov. is distinguished from the members of this clade mainly by the shape of its humeral spot, possessing few irregular inconspicuous vertically arranged chromatophores in the humeral region, or sometimes a very thin and inconspicuous humeral spot, and other characters related to teeth count, and color pattern. The phylogenetic position of the new species within the rosy tetra clade was based on molecular phylogenetic analysis using sequences of the mitochondrial gene cytochrome oxidase subunit 1. In addition, a new clade (here termed Hyphessobryconmicropterus clade) within the rosy tetra clade is proposed based on molecular data, comprising H.carusp. nov., H.micropterus, H.piorskii, and H.simulatus, and with H.carusp. nov. and H.piorskii recovered as sister species. Our results suggest cryptic speciation in the rosy tetra clade and, more specifically, in the H.micropterus clade. We recommend the use of integrative taxonomy for future taxonomic revisions and species descriptions when dealing with species complexes and groups containing possible cryptic species.
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16
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Cunha MS, Fregonezi AR, Fava L, Hilsdorf AWS, Campos LAO, Dergam JA. Phylogeography and Historical Biogeography of the Astyanax bimaculatus Species Complex (Teleostei: Characidae) in Coastal Southeastern South America. Zebrafish 2019; 16:115-127. [DOI: 10.1089/zeb.2018.1668] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Affiliation(s)
- Marina S. Cunha
- Departamento de Biologia Animal, Universidade Federal de Viçosa, Viçosa, Brazil
- Departamento de Biologia Geral, Universidade Federal de Viçosa, Viçosa, Brazil
| | - Aline R. Fregonezi
- Departamento de Biologia Geral, Universidade Federal de Viçosa, Viçosa, Brazil
| | - Lucioni Fava
- Departamento de Biologia Animal, Universidade Federal de Viçosa, Viçosa, Brazil
| | | | - Lucio A. O. Campos
- Departamento de Biologia Geral, Universidade Federal de Viçosa, Viçosa, Brazil
| | - Jorge A. Dergam
- Departamento de Biologia Animal, Universidade Federal de Viçosa, Viçosa, Brazil
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17
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Landínez-García RM, Marquez EJ. Microsatellite loci development and population genetics in Neotropical fish Curimata mivartii (Characiformes: Curimatidae). PeerJ 2018; 6:e5959. [PMID: 30479905 PMCID: PMC6238776 DOI: 10.7717/peerj.5959] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2018] [Accepted: 10/18/2018] [Indexed: 11/20/2022] Open
Abstract
The Curimatidae family plays an ecological role in the recycling and distribution of nutrients and constitutes a major food source for several commercially important fishes. Curimata mivartii, a member of this family, is considered a short-distance migratory species (≤100 km), categorized by the International Union for Conservation of Nature as a near threatened species, based on its declining population densities and habitat disturbance and fragmentation. Since population genetics and species-specific molecular tools remain unknown for all members of the Curimatidae family, this study developed a set of microsatellite loci and studied the population genetics of C. mivartii in the lower section of the Colombian Magdalena-Cauca basin. The results showed high levels of genetic diversity and evidence of gene flow even between locations separated over 350 km. This information provides a baseline for designing conservation and management programs for C.mivartii and constitutes the first study of population genetics in Curimatidae.
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Affiliation(s)
- Ricardo M Landínez-García
- Laboratorio de Biología Molecular y Celular, Facultad de Ciencias, Escuela de Biociencias, Universidad Nacional de Colombia-Sede Medellín, Medellín, Colombia
| | - Edna J Marquez
- Laboratorio de Biología Molecular y Celular, Facultad de Ciencias, Escuela de Biociencias, Universidad Nacional de Colombia-Sede Medellín, Medellín, Colombia
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18
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Molecular phylogenetics of Neotropical detritivorous fishes of the family Curimatidae (Teleostei: Characiformes). Mol Phylogenet Evol 2018; 127:800-812. [DOI: 10.1016/j.ympev.2018.06.027] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2018] [Revised: 06/12/2018] [Accepted: 06/15/2018] [Indexed: 11/19/2022]
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19
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Bonilla-Castillo CA, Córdoba EA, Gómez G, Duponchelle F. Population dynamics of Prochilodus nigricans (Characiformes: Prochilodontidae) in the Putumayo River. NEOTROPICAL ICHTHYOLOGY 2018. [DOI: 10.1590/1982-0224-20170139] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
ABSTRACT The black prochilodus (Prochilodus nigricans) is one of the most landed scaled fish species of the middle and upper parts of the Putumayo River, in the tri-national area between Colombia, Ecuador and Peru. Despite its importance, biological information about this species is too scant to guide fisheries management in this portion of the Colombian Amazon. In this study, 10884 individuals were sampled in the fish markets of Puerto Leguízamo between 2009 and 2017. This sampling was used to document reproductive patterns, but also growth and mortality parameters from length frequency distributions. The size at which all fish were mature was 22 cm Ls, which should be the established as the minimum size of capture to ensure that all fish have had a chance to reproduce before being caught. Growth and mortality parameters indicated a slower growth in the Putumayo than in other Amazonian rivers and a relatively high exploitation rate.
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Affiliation(s)
- César A. Bonilla-Castillo
- Instituto Amazónico de Investigaciones Científicas, Colombia; Institut de Recherche pour le Développement, France
| | - Edwin Agudelo Córdoba
- Instituto Amazónico de Investigaciones Científicas, Colombia; Institut de Recherche pour le Développement, France
| | - Guber Gómez
- Instituto Amazónico de Investigaciones Científicas, Colombia; Institut de Recherche pour le Développement, France
| | - Fabrice Duponchelle
- Institut de Recherche pour le Développement, France; Institut de Recherche pour le Développement, France
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20
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Lemopoulos A, Covain R. Biogeography of the freshwater fishes of the Guianas using a partitioned parsimony analysis of endemicity with reappraisal of ecoregional boundaries. Cladistics 2018; 35:106-124. [DOI: 10.1111/cla.12341] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/06/2018] [Indexed: 11/29/2022] Open
Affiliation(s)
- Alexandre Lemopoulos
- Department of Environmental and Biological Sciences; University of Eastern Finland; PO Box 111 Joensuu FI-80220 Finland
- Department of Herpetology and Ichthyology; Museum of Natural History; PO Box 6434 Geneva 6 CH-1211 Switzerland
| | - Raphaël Covain
- Department of Herpetology and Ichthyology; Museum of Natural History; PO Box 6434 Geneva 6 CH-1211 Switzerland
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21
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Melo BF, Dorini BF, Foresti F, Oliveira C. Little Divergence Among Mitochondrial Lineages of Prochilodus (Teleostei, Characiformes). Front Genet 2018; 9:107. [PMID: 29670644 PMCID: PMC5893770 DOI: 10.3389/fgene.2018.00107] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2017] [Accepted: 03/19/2018] [Indexed: 11/13/2022] Open
Abstract
Evidence that migration prevents population structure among Neotropical characiform fishes has been reported recently but the effects upon species diversification remain unclear. Migratory species of Prochilodus have complex species boundaries and intrincate taxonomy representing a good model to address such questions. Here, we analyzed 147 specimens through barcode sequences covering all species of Prochilodus across a broad geographic area of South America. Species delimitation and population genetic methods revealed very little genetic divergence among mitochondrial lineages suggesting that extensive gene flow resulted likely from the highly migratory behavior, natural hybridization or recent radiation prevent accumulation of genetic disparity among lineages. Our results clearly delimit eight genetic lineages in which four of them contain a single species and four contain more than one morphologically problematic taxon including a trans-Andean species pair and species of the P. nigricans group. Information about biogeographic distribution of haplotypes presented here might contribute to further research on the population genetics and taxonomy of Prochilodus.
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Affiliation(s)
- Bruno F. Melo
- Departamento de Morfologia, Instituto de Biociências, Universidade Estadual Paulista, Botucatu, Brazil
- Department of Vertebrate Zoology, National Museum of Natural History, Smithsonian Institution, Washington, DC, United States
| | - Beatriz F. Dorini
- Departamento de Morfologia, Instituto de Biociências, Universidade Estadual Paulista, Botucatu, Brazil
| | - Fausto Foresti
- Departamento de Morfologia, Instituto de Biociências, Universidade Estadual Paulista, Botucatu, Brazil
| | - Claudio Oliveira
- Departamento de Morfologia, Instituto de Biociências, Universidade Estadual Paulista, Botucatu, Brazil
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22
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Silva-Santos R, Ramirez JL, Galetti PM, Freitas PD. Molecular Evidences of a Hidden Complex Scenario in Leporinus cf. friderici. Front Genet 2018; 9:47. [PMID: 29497440 PMCID: PMC5818402 DOI: 10.3389/fgene.2018.00047] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2017] [Accepted: 01/31/2018] [Indexed: 12/11/2022] Open
Abstract
The megadiversity of the neotropical ichthyofauna has been associated to recent diversification processes, reflecting in subtle or lacking morphological differentiation between species, challenging the classical taxonomic identification. Leporinus friderici occurs in several river basins of South America, and its nominal taxonomic validity has been questioned. Its wide distribution within the Brazilian Shield suggests that this species could be genetically structured among the hydrographic basins, despite a sharp morphological similarity. In this study, we performed phylogenetic analyses, based on three nuclear (recombination activating gene 1, RAG1, recombination activating gene 2, RAG2, and myosin heavy chain 6 cardiac muscle alpha gene, Myh6) and two mitochondrial (COI and Cytochrome b, Cytb) markers, in specimens morphologically similar to L. friderici and related species from different hydrographic basins in South America. Our phylogenetic tree identified four well-supported clades, which point out to the existence of taxonomic inconsistencies within this fish group. A clade named L. cf. friderici sensu stricto included eight Molecular Operational Taxonomic Units recently diversified in the Brazilian Shield basins. These results were also confirmed by a single-gene species delimitation analysis. It is suggested that this clade includes a species complex, characterizing taxonomic uncertainties. Another clade recovered only L. friderici from the Suriname rivers, validating this nominal species in its type locality. A third no-named clade, characterized by deeper species divergence, recovered five different nominal species interleaved with other undescribed forms previously also recognized as L. cf. friderici, indicating taxonomic errors. The fourth clade only included L. taeniatus. Our results showed a complex scenario involving the morphotype L. cf. friderici and allowed us to address aspects related to evolutionary diversification of this fish group and historical processes involved with, highlighting the importance of revealing hidden biodiversity for the taxonomy and conservationist action plans of these fish.
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Affiliation(s)
- Rosane Silva-Santos
- Laboratório de Biodiversidade Molecular e Conservação, Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Paulo, Brazil
| | - Jorge L Ramirez
- Laboratório de Biodiversidade Molecular e Conservação, Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Paulo, Brazil
| | - Pedro M Galetti
- Laboratório de Biodiversidade Molecular e Conservação, Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Paulo, Brazil
| | - Patrícia D Freitas
- Laboratório de Biodiversidade Molecular e Conservação, Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Paulo, Brazil
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23
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Carvalho ML, Costa Silva GJD, Melo S, Ashikaga FY, Shimabukuro-Dias CK, Scacchetti PC, Devidé R, Foresti F, Oliveira C. The non-monotypic status of the neotropical fish genus Hemiodontichthys (Siluriformes, Loricariidae) evidenced by genetic approaches. Mitochondrial DNA A DNA Mapp Seq Anal 2018; 29:1224-1230. [DOI: 10.1080/24701394.2018.1431230] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Affiliation(s)
- Margarida Lima Carvalho
- Laboratório de Citogenética e Genética Molecular – LABGENE, Universidade Federal do Acre, Rio Branco, Acre, Brazil
| | - Guilherme José da Costa Silva
- Instituto de Biociências de Botucatu, Laboratório de Biologia e Genética de Peixes – LBGP, Universidade Estadual Paulista “Júlio de Mesquita Filho”, Botucatu, São Paulo, Brazil
- Departamento de Biologia, Universidade Santo Amaro São Paulo, Brazil
| | - Silvana Melo
- Instituto de Biociências de Botucatu, Laboratório de Biologia e Genética de Peixes – LBGP, Universidade Estadual Paulista “Júlio de Mesquita Filho”, Botucatu, São Paulo, Brazil
| | - Fernando Yuldi Ashikaga
- Instituto de Biociências de Botucatu, Laboratório de Biologia e Genética de Peixes – LBGP, Universidade Estadual Paulista “Júlio de Mesquita Filho”, Botucatu, São Paulo, Brazil
| | - Cristiane Kioko Shimabukuro-Dias
- Instituto de Biociências de Botucatu, Laboratório de Biologia e Genética de Peixes – LBGP, Universidade Estadual Paulista “Júlio de Mesquita Filho”, Botucatu, São Paulo, Brazil
| | - Priscilla Cardim Scacchetti
- Instituto de Biociências de Botucatu, Laboratório de Biologia e Genética de Peixes – LBGP, Universidade Estadual Paulista “Júlio de Mesquita Filho”, Botucatu, São Paulo, Brazil
| | - Renato Devidé
- Instituto de Biociências de Botucatu, Laboratório de Biologia e Genética de Peixes – LBGP, Universidade Estadual Paulista “Júlio de Mesquita Filho”, Botucatu, São Paulo, Brazil
| | - Fausto Foresti
- Instituto de Biociências de Botucatu, Laboratório de Biologia e Genética de Peixes – LBGP, Universidade Estadual Paulista “Júlio de Mesquita Filho”, Botucatu, São Paulo, Brazil
| | - Claudio Oliveira
- Instituto de Biociências de Botucatu, Laboratório de Biologia e Genética de Peixes – LBGP, Universidade Estadual Paulista “Júlio de Mesquita Filho”, Botucatu, São Paulo, Brazil
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24
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Introgression from non-native species unveils a hidden threat to the migratory Neotropical fish Prochilodus hartii. Biol Invasions 2017. [DOI: 10.1007/s10530-017-1556-4] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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25
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Melo S, Utsunomia R, Penitente M, Sobrinho-Scudeler PE, Porto-Foresti F, Oliveira C, Foresti F, Dergam JA. B chromosome dynamics in Prochilodus costatus (Teleostei, Characiformes) and comparisons with supernumerary chromosome system in other Prochilodus species. COMPARATIVE CYTOGENETICS 2017; 11:393-403. [PMID: 28919971 PMCID: PMC5596993 DOI: 10.3897/compcytogen.v11i2.12784] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/18/2017] [Accepted: 04/13/2017] [Indexed: 06/07/2023]
Abstract
Within the genus Prochilodus Agassiz, 1829, five species are known to carry B chromosomes, i.e. chromosomes beyond the usual diploid number that have been traditionally considered as accessory for the genome. Chromosome microdissection and mapping of repetitive DNA sequences are effective tools to assess the DNA content and allow a better understanding about the origin and composition of these elements in an array of species. In this study, a novel characterization of B chromosomes in Prochilodus costatus Valenciennes, 1850 (2n=54) was reported for the first time and their sequence complementarity with the supernumerary chromosomes observed in Prochilodus lineatus (Valenciennes, 1836) and Prochilodus argenteus Agassiz, 1829 was investigated. The hybridization patterns obtained with chromosome painting using the micro B probe of P. costatus and the satDNA SATH1 mapping made it possible to assume homology of sequences between the B chromosomes of these congeneric species. Our results suggest that the origin of B chromosomes in the genus Prochilodus is a phylogenetically old event.
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Affiliation(s)
- Silvana Melo
- Departamento de Biologia Animal, Campus Universitário, Universidade Federal de Viçosa, 36570-000, Viçosa, Minas Gerais, Brazil
- Departamento de Morfologia, Instituto de Biociências, Universidade Estadual Paulista, Distrito de Rubião Junior, s/n, 18618-689, Botucatu, São Paulo, Brazil
| | - Ricardo Utsunomia
- Departamento de Morfologia, Instituto de Biociências, Universidade Estadual Paulista, Distrito de Rubião Junior, s/n, 18618-689, Botucatu, São Paulo, Brazil
| | - Manolo Penitente
- Departamento de Ciências Biológicas, Faculdade de Ciências, Universidade Estadual Paulista, Campus de Bauru, 17033-360 Bauru, São Paulo, Brazil
| | - Patrícia Elda Sobrinho-Scudeler
- Departamento de Morfologia, Instituto de Biociências, Universidade Estadual Paulista, Distrito de Rubião Junior, s/n, 18618-689, Botucatu, São Paulo, Brazil
| | - Fábio Porto-Foresti
- Departamento de Ciências Biológicas, Faculdade de Ciências, Universidade Estadual Paulista, Campus de Bauru, 17033-360 Bauru, São Paulo, Brazil
| | - Claudio Oliveira
- Departamento de Morfologia, Instituto de Biociências, Universidade Estadual Paulista, Distrito de Rubião Junior, s/n, 18618-689, Botucatu, São Paulo, Brazil
| | - Fausto Foresti
- Departamento de Morfologia, Instituto de Biociências, Universidade Estadual Paulista, Distrito de Rubião Junior, s/n, 18618-689, Botucatu, São Paulo, Brazil
| | - Jorge Abdala Dergam
- Departamento de Biologia Animal, Campus Universitário, Universidade Federal de Viçosa, 36570-000, Viçosa, Minas Gerais, Brazil
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26
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Willis SC. One species or four? Yes!...and, no. Or, arbitrary assignment of lineages to species obscures the diversification processes of Neotropical fishes. PLoS One 2017; 12:e0172349. [PMID: 28235096 PMCID: PMC5325279 DOI: 10.1371/journal.pone.0172349] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2016] [Accepted: 02/03/2017] [Indexed: 11/18/2022] Open
Abstract
Species are fundamental units in many biological disciplines, but there is continuing disagreement as to what species are, how to define them, and even whether the concept is useful. While some of this debate can be attributed to inadequate data and insufficient statistical frameworks in alpha taxonomy, an equal part results from the ambiguity over what species are expected to represent by the many who use them. Here, mtDNA data, microsatellite data, and sequence data from 17 nuclear loci are used in an integrated and quantitative manner to resolve the presence of evolutionary lineages, their contemporary and historical structure, and their correspondence to species, in a species complex of Amazonian peacock "bass" cichlids (Cichla pinima sensu lato). Results suggest that the historical narrative for these populations is more complex than can be portrayed by recognizing them as one, two, or four species: their history and contemporary dynamics cannot be unambiguously rendered as discrete units (taxa) at any level without both choosing the supremacy of one delimitation criterion and obscuring the very information that provides insight into the diversification process. This calls into question the utility of species as a rank, term, or concept, and suggests that while biologists may have a reasonable grasp of the structure of evolution, our methods of conveying these insights need updating. The lack of correspondence between evolutionary phenomena and discrete species should serve as a null hypothesis, and researchers should focus on quantifying the diversity in nature at whatever hierarchical level it occurs.
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Affiliation(s)
- Stuart C. Willis
- Department of Life Sciences, Texas A&M University-Corpus Christi, Corpus Christi, Texas, United States of America
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27
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Burns MD, Chatfield M, Birindelli JLO, Sidlauskas BL. Systematic assessment of the Leporinus desmotes species complex, with a description of two new species. NEOTROPICAL ICHTHYOLOGY 2017. [DOI: 10.1590/1982-0224-20160166] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
ABSTRACT Members of the Leporinus desmotes species complex can be distinguished from other barred or banded congeners by the combination of nine distinct black bars across the head and trunk and long, pointed, laterally compressed and upward curving symphyseal dentary teeth. A taxonomic reassessment of this complex revealed two new species, one from the Orinoco and Negro rivers of Venezuela and Brazil, and the other from the Xingu and Tapajós rivers of Brazil. Both species are similar to L. desmotes and L. jatuncochi, but differ significantly in body shape morphology, coloration, and/or circumpeduncular scale counts. Genetic evidence also contributes to the recognition of both new species. This contribution also maps the geographic distribution of the four known species, and highlights the presence of an unusual meristic polymorphism within Leporinus desmotes sensu stricto that may suggest the presence of even more unrecognized diversity.
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Tursellino MN, Silva DMZDA, Abad CQ, Blacio WAM, Romero ORS, Oliveira C. First cytogenetic analysis of Ichthyoelephas humeralis (Günther, 1860) by conventional and molecular methods with comments on the karyotypic evolution in Prochilodontidae. COMPARATIVE CYTOGENETICS 2016; 10:615-624. [PMID: 28123682 PMCID: PMC5240513 DOI: 10.3897/compcytogen.v10i4.9858] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/13/2016] [Accepted: 09/08/2016] [Indexed: 06/06/2023]
Abstract
We used conventional cytogenetic techniques (Giemsa, C-banding, Ag-NOR), and fluorescent in situ hybridization (FISH) with 5S and 18S rDNA probes to investigate the karyotype and cytogenetic characteristics of Ichthyoelephas humeralis (Günther, 1860) from Ecuador. The specimens studied have a karyotype with 2n=54 biarmed chromosomes (32 M + 22 SM) and C-positive heterochromatin located on the centromeric, pericentromeric, interstitial, and terminal regions of some chromosomes. The nucleolus organizer regions occurred terminally on the long arm of chromosome pair 2. FISH confirmed the presence of only one 18S rDNA cluster with nonsyntenic localization with the 5S rDNA. Cytogenetic data allow us to refute the earlier morphological hypothesis of a sister relationship between Semaprochilodus Fowler, 1941 and Ichthyoelephas Posada Arango, 1909 and support the molecular proposal that Ichthyoelephas is a sister group to the monophyletic clade containing Prochilodus Agassiz, 1829 and Semaprochilodus.
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Affiliation(s)
- Mauro Nirchio Tursellino
- Universidad Técnica de Machala, Facultad de Ciencias Agropecuarias, Av. Panamericana Km 51/2, Vía Machala Pasaje, El Oro, Ecuador
- Universidad de Oriente, Escuela de Ciencias Aplicadas del Mar, Boca de Río, Península de Macanao, Estado Nueva Esparta, Venezuela
| | - Duílio Mazzoni Zerbinato de Andrade Silva
- Laboratório de Biologia e Genética de Peixes, Instituto de Biociências de Botucatu, Universidade Estadual Paulista (UNESP), Departamento de Morfologia, Distrito de Rubião Junior, Botucatu, São Paulo, Brazil. CEP: 18618-689
| | - César Quezada Abad
- Universidad Técnica de Machala, Facultad de Ciencias Agropecuarias, Av. Panamericana Km 51/2, Vía Machala Pasaje, El Oro, Ecuador
| | - Wilmer Arnoldo Moreira Blacio
- Universidad Técnica de Machala, Facultad de Ciencias Agropecuarias, Av. Panamericana Km 51/2, Vía Machala Pasaje, El Oro, Ecuador
| | - Omar Rogerio Sánchez Romero
- Universidad Técnica de Machala, Facultad de Ciencias Agropecuarias, Av. Panamericana Km 51/2, Vía Machala Pasaje, El Oro, Ecuador
| | - Claudio Oliveira
- Laboratório de Biologia e Genética de Peixes, Instituto de Biociências de Botucatu, Universidade Estadual Paulista (UNESP), Departamento de Morfologia, Distrito de Rubião Junior, Botucatu, São Paulo, Brazil. CEP: 18618-689
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Frable BW, Melo BF, Sidlauskas BL, Hoekzema K, Vari RP, Oliveira C. Data on the multilocus molecular phylogenies of the Neotropical fish family Prochilodontidae (Teleostei: Characiformes). Data Brief 2016; 9:128-42. [PMID: 27642619 PMCID: PMC5018087 DOI: 10.1016/j.dib.2016.08.015] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2016] [Revised: 08/01/2016] [Accepted: 08/08/2016] [Indexed: 11/26/2022] Open
Abstract
The data presented herein support the article "Molecular phylogenetics of the Neotropical fish family Prochilodontidae (Teleostei: Characiformes)" (B.F. Melo, B.L. Sidlauskas, B.W. Frable, K. Hoekzema, R.P. Vari, C. Oliveira, 2016) [1], which inferred phylogenetic relationships of the prochilodontids from an alignment of three mitochondrial and three nuclear loci (5279 bp) for all 21 recognized prochilodontid species and 22 related species. Herein, we provide primer sequences, museum voucher information and GenBank accession numbers. Additionally, we more fully describe the maximum-likelihood and Bayesian phylogenetic analyses of the concatenated dataset, detail the Bayesian species tree analysis, and provide the maximum likelihood topologies congruent with prior morphological hypotheses that were compared with the unconstrained tree using Shimodaira-Hasegawa tests.
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Affiliation(s)
- Benjamin W Frable
- Department of Fisheries and Wildlife, Oregon State University, Corvallis, OR, USA; Marine Vertebrate Collection, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, CA, USA
| | - Bruno F Melo
- Departamento de Morfologia, Instituto de Biociências, Universidade Estadual Paulista, Botucatu, São Paulo, Brazil; Department of Vertebrate Zoology, National Museum of Natural History, Smithsonian Institution, Washington, DC, USA
| | - Brian L Sidlauskas
- Department of Fisheries and Wildlife, Oregon State University, Corvallis, OR, USA; Department of Vertebrate Zoology, National Museum of Natural History, Smithsonian Institution, Washington, DC, USA
| | - Kendra Hoekzema
- Department of Fisheries and Wildlife, Oregon State University, Corvallis, OR, USA
| | - Richard P Vari
- Department of Vertebrate Zoology, National Museum of Natural History, Smithsonian Institution, Washington, DC, USA
| | - Claudio Oliveira
- Departamento de Morfologia, Instituto de Biociências, Universidade Estadual Paulista, Botucatu, São Paulo, Brazil
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