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Gavazzoni M, Brezinski FC, Pedroso TH, Pavanelli CS, Graça WJD, Blanco DR, Lui RL, Margarido VP. Integrative Taxonomy Suggests Resurrection of Species of the Astyanax bimaculatus Group (Characiformes, Characidae). Zebrafish 2024. [PMID: 38980839 DOI: 10.1089/zeb.2024.0132] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/11/2024] Open
Abstract
Using integrative tools can be effective for species identification, especially in complex groups like Astyanax. Astyanax bimaculatus group is composed of six valid species, including A. lacustris. "A. altiparanae", "A. asuncionensis", and "A. jacuhiensis" are considered as junior synonyms of A. lacustris. Seeking to test the operational taxonomic unit (OTU) status of the junior synonyms of A. lacustris ("A. altiparanae", "A. asuncionensis", and "A. jacuhiensis"), we used analyses through mitochondrial DNA (COI and Cytb), cytogenetic markers (classical and molecular), and morphometry ("truss network"). Analysis of mitochondrial DNA sequences separated A. lacustris from the other synonymized species. The cytogenetic and morphometric analyses did not corroborate the synonymization and suggest that besides A. lacustris, the OTUs A. altiparanae, A. asuncionensis, and A. jacuhiensis are valid species. The analysis of different characters proposed by the integrative taxonomy used on the same individuals could provide greater reliability and minimize the underestimation of biodiversity.
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Affiliation(s)
- Mariane Gavazzoni
- Universidade Estadual do Oeste do Paraná, Pós-Graduação em Conservação e Manejo de Recursos Naturais, Cascavel, Brazil
| | - Flavia C Brezinski
- Universidade Estadual do Oeste do Paraná, Pós-Graduação em Conservação e Manejo de Recursos Naturais, Cascavel, Brazil
| | - Thiago H Pedroso
- Universidade Estadual de Maringá, Programa de Pós-Graduação em Ecologia de Ambientes Aquáticos Continentais, Maringá, Brazil
| | - Carla S Pavanelli
- Universidade Estadual de Maringá, Programa de Pós-Graduação em Ecologia de Ambientes Aquáticos Continentais, Maringá, Brazil
- Universidade Estadual de Maringá, Centro de Ciências Biológicas, Núcleo de Pesquisas em Limnologia, Ictiologia e Aquicultura, Maringá, Brazil
| | - Weferson J da Graça
- Universidade Estadual de Maringá, Programa de Pós-Graduação em Ecologia de Ambientes Aquáticos Continentais, Maringá, Brazil
- Universidade Estadual de Maringá, Centro de Ciências Biológicas, Núcleo de Pesquisas em Limnologia, Ictiologia e Aquicultura, Maringá, Brazil
- Departamento de Biologia, Universidade Estadual de Maringá, Centro de Ciências Biológicas, Maringá, Brazil
| | - Daniel R Blanco
- Universidade Tecnológica Federal do Paraná, Campus Santa Helena, Santa Helena, Brazil
| | - Roberto L Lui
- Universidade Estadual do Oeste do Paraná, Pós-Graduação em Conservação e Manejo de Recursos Naturais, Cascavel, Brazil
| | - Vladimir P Margarido
- Universidade Estadual do Oeste do Paraná, Pós-Graduação em Conservação e Manejo de Recursos Naturais, Cascavel, Brazil
- Universidade Estadual de Maringá, Programa de Pós-Graduação em Ecologia de Ambientes Aquáticos Continentais, Maringá, Brazil
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Muhala V, Guimarães-Costa A, Macate IE, Rabelo LP, Bessa-Silva AR, Watanabe L, dos Santos GD, Sambora L, Vallinoto M, Sampaio I. DNA barcoding for the assessment of marine and coastal fish diversity from the Coast of Mozambique. PLoS One 2024; 19:e0293345. [PMID: 38319915 PMCID: PMC10846724 DOI: 10.1371/journal.pone.0293345] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2023] [Accepted: 10/10/2023] [Indexed: 02/08/2024] Open
Abstract
The ichthyological provinces of Mozambique are understudied hotspots of global fish diversity. In this study, we applied DNA barcoding to identify the composition of the fish fauna from the coast of Mozambique. A total of 143 species belonging to 104 genera, 59 families, and 30 orders were identified. The overall K2P distance of the COI sequences within species ranged from 0.00% to 1.51%, while interspecific distances ranged from 3.64% to 24.49%. Moreover, the study revealed 15 threatened species according to the IUCN Red List of Threatened Species, with elasmobranchs being the most represented group. Additionally, the study also uncovered four new species that were not previously recorded in this geographic area, including Boleophthalmus dussumieri, Maculabatis gerrardi, Hippocampus kelloggi, and Lethrinus miniatus. This study represents the first instance of utilizing molecular references to explore the fish fauna along the Mozambican coast. Our results indicate that DNA barcoding is a dependable technique for the identification and delineation of fish species in the waters of Mozambique. The DNA barcoding library established in this research will be an invaluable asset for advancing the understanding of fish diversity and guiding future conservation initiatives.
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Affiliation(s)
- Valdemiro Muhala
- Laboratório de Evolução, Universidade Federal do Pará, Alameda Leandro Ribeiro, Aldeia, Bragança, Pará, Brazil
- Divisão de Agricultura, Instituto Superior Politécnico de Gaza, Chókwè, Mozambique
| | - Aurycéia Guimarães-Costa
- Laboratório de Evolução, Universidade Federal do Pará, Alameda Leandro Ribeiro, Aldeia, Bragança, Pará, Brazil
| | - Isadola Eusébio Macate
- Laboratório de Evolução, Universidade Federal do Pará, Alameda Leandro Ribeiro, Aldeia, Bragança, Pará, Brazil
- Departamento de Ciências Agrárias e Ambientais, Universidade Estadual de Santa Cruz, Ilheus, BA, Brazil
| | - Luan Pinto Rabelo
- Laboratório de Evolução, Universidade Federal do Pará, Alameda Leandro Ribeiro, Aldeia, Bragança, Pará, Brazil
| | - Adam Rick Bessa-Silva
- Laboratório de Evolução, Universidade Federal do Pará, Alameda Leandro Ribeiro, Aldeia, Bragança, Pará, Brazil
| | - Luciana Watanabe
- Laboratório de Evolução, Universidade Federal do Pará, Alameda Leandro Ribeiro, Aldeia, Bragança, Pará, Brazil
| | - Gisele Damasceno dos Santos
- Laboratório de Evolução, Universidade Federal do Pará, Alameda Leandro Ribeiro, Aldeia, Bragança, Pará, Brazil
| | - Luísa Sambora
- Departamento de Produção Agrária, Escola Superior de Desenvolvimento Rural, Universidade Eduardo Mondlane, Vilankulos, Moçambique
| | - Marcelo Vallinoto
- Laboratório de Evolução, Universidade Federal do Pará, Alameda Leandro Ribeiro, Aldeia, Bragança, Pará, Brazil
| | - Iracilda Sampaio
- Laboratório de Evolução, Universidade Federal do Pará, Alameda Leandro Ribeiro, Aldeia, Bragança, Pará, Brazil
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Morais-Silva JP, Scorsim B, Gonçalves G, Frota A, da Graça WJ, de Oliveira AV. Molecular Markers Reveal a New and Possibly Threatened Species of Cnesterodon (Poeciliidae, Cnesterodontini) from the Upper Paraná River Basin, Brazil. Zebrafish 2023; 20:37-45. [PMID: 36695733 PMCID: PMC9968864 DOI: 10.1089/zeb.2022.0052] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
Cnesterodon comprises 10 valid species occurring in the major river basins of South America. Recent ichthyofaunistic studies in the Ivaí River basin, upper Paraná River system, suggested the existence of a possible new species, which was identified as Cnesterodon sp. based on morphological characters. Currently, the use of molecular tools has proved to be fundamental in aiding phylogenetics and cataloging biodiversity; therefore, in this study, we molecularly characterize a possible new species of Cnesterodon from the Ivaí River basin encoding the mitochondrial genes Cytochrome c Oxidase, subunit I (COI), and NADH dehydrogenase subunit 2 (ND2). The genetic differences found showed that this species really differs from the other Cnesterodon species, indicating that it is a distinct species, which is possibly already in serious danger of extinction since its habitat often suffers from human exploitation and its distribution is restricted to only two sites in the upper Ivaí River basin, but it has disappeared in one of them.
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Affiliation(s)
- João Paulo Morais-Silva
- Programa de Pós-Graduação em Ecologia de Ambientes Aquáticos Continentais, Departamento de Biologia, Centro de Ciências Biológicas, Universidade Estadual de Maringá (UEM), Maringá, Brazil
| | - Bárbara Scorsim
- Programa de Pós-Graduação em Ecologia de Ambientes Aquáticos Continentais, Departamento de Biologia, Centro de Ciências Biológicas, Universidade Estadual de Maringá (UEM), Maringá, Brazil
| | - Geovana Gonçalves
- Curso de Graduação em Ciências Biológicas, Departamento de Biologia, Centro de Ciências Biológicas, Universidade Estadual de Maringá (UEM), Maringá, Brazil
| | - Augusto Frota
- Programa de Pós-Graduação em Ecologia de Ambientes Aquáticos Continentais, Departamento de Biologia, Centro de Ciências Biológicas, Universidade Estadual de Maringá (UEM), Maringá, Brazil
| | - Weferson Júnio da Graça
- Programa de Pós-Graduação em Ecologia de Ambientes Aquáticos Continentais, Departamento de Biologia, Centro de Ciências Biológicas, Universidade Estadual de Maringá (UEM), Maringá, Brazil
- Departamento de Biologia and Núcleo de Pesquisas em Limnologia, Ictiologia e Aquicultura (Nupélia), Centro de Ciências Biológicas, Universidade Estadual de Maringá (UEM). Maringá, Brazil
- Departamento de Biologia, Programa de Pós-Graduação em Biologia Comparada, Centro de Ciências Biológicas, Universidade Estadual de Maringá (UEM). Maringá, Brazil
| | - Alessandra Valéria de Oliveira
- Programa de Pós-Graduação em Ecologia de Ambientes Aquáticos Continentais, Departamento de Biologia, Centro de Ciências Biológicas, Universidade Estadual de Maringá (UEM), Maringá, Brazil
- Departamento de Biotecnologia, Genética e Biologia Celular and Núcleo de Pesquisas em Limnologia, Ictiologia e Aquicultura (Nupélia), Centro de Ciências Biológicas, Universidade Estadual de Maringá (UEM). Maringá, Brazil
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OUP accepted manuscript. Zool J Linn Soc 2022. [DOI: 10.1093/zoolinnean/zlac018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
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Azambuja M, Marcondes DS, Nogaroto V, Moreira-Filho O, Vicari MR. Population structuration and chromosomal features homogeneity in Parodon nasus (Characiformes: Parodontidae): A comparison between Lower and Upper Paraná River representatives. NEOTROPICAL ICHTHYOLOGY 2022. [DOI: 10.1590/1982-0224-2021-0162] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
ABSTRACT The ichthyofauna of the La Plata hydrographic basin is divided into Upper and Lower Paraná River systems due to the geographic isolation of the Sete Quedas waterfalls, currently flooded by the lake of the Itaipu dam. In Parodontidae, pairs of species, or groups of cryptic species were described between these systems. Although genetic isolation and speciation have already been proposed in other species in the group, Parodon nasus has been maintained as a valid species and distributed throughout the La Plata river basin. In this perspective, specimens of P. nasus from four different sampling sites in the Upper and Lower Paraná River systems were compared regarding the karyotypes, molecular analyzes of population biology and species delimitation to investigate their genetic and population isolation in the La Plata river basin. Despite a geographic barrier and the immense geographic distance separating the specimens sampled from the Lower Paraná River system compared to those from the Upper Paraná River, the data obtained showed P. nasus as a unique taxon. Thus, unlike other species of Parodontidae that showed diversification when comparing the groups residing in the Lower versus Upper Paraná River, P. nasus showed a population structure and a karyotypic homogeneity.
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Abstract
Since their inception, DNA barcodes have become a powerful tool for understanding the biodiversity and biology of aquatic species, with multiple applications in diverse fields such as food security, fisheries, environmental DNA, conservation, and exotic species detection. Nevertheless, most aquatic ecosystems, from marine to freshwater, are understudied, with many species disappearing due to environmental stress, mostly caused by human activities. Here we highlight the progress that has been made in studying aquatic organisms with DNA barcodes, and encourage its further development in assisting sustainable use of aquatic resources and conservation.
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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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8
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Reis VJC, Dos Santos SA, Britto MR, de Assis Volpi T, de Pinna MCC. Iterative taxonomy reveals a new species of Trichomycterus Valenciennes 1832 (Siluriformes, Trichomycteridae) widespread in Rio Doce basin: a pseudocryptic of T. immaculatus. JOURNAL OF FISH BIOLOGY 2020; 97:1607-1623. [PMID: 32779738 DOI: 10.1111/jfb.14490] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Revised: 07/31/2020] [Accepted: 08/05/2020] [Indexed: 06/11/2023]
Abstract
This paper reports on a new species of Trichomycterus from the Rio Doce basin. Unusually for new taxa in the genus during the past few decades, the new species is not narrowly endemic but instead widely distributed in its major drainage, the Rio Doce. The species has been collected and deposited in scientific collections for some years, but has been systematically misidentified as the more abundant Trichomycterus immaculatus or, to a lesser degree, as other morphologically similar species from south-eastern Brazil such as T. nigricans and T. pradensis. A combination of several morphological characteristics, such as vertebral number, pectoral-fin ray counts, pigmentation pattern and barcoding distance, were iteratively used and unambiguously distinguish the new species from all congeners. The present case reveals a pattern of diversity-discovery in which rare and narrowly endemic morphologically conspicuous species are discovered and described before visually inconspicuous taxa, even when the latter are more abundant and widespread. The morphological similarities among south-eastern Brazilian species with a uniform dark-grey color serve as basis for a brief discussion about the concepts of cryptic and pseudo-cryptic species in Trichomycterus and their consequences for potentially hidden diversity in the genus.
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Affiliation(s)
- Vinícius J C Reis
- Museu de Zoologia da Universidade de São Paulo, 481 Av. Nazaré, São Paulo, São Paulo, 04263-000, Brazil
- Institut de Systématique, Evolution, Biodiversité, Muséum national d'Histoire naturelle, CNRS, Sorbonne Université, EPHE, Université des Antilles CP 30, Paris, France
| | - Sergio A Dos Santos
- Museu Nacional, Universidade Federal do Rio de Janeiro, Quinta da Boa Vista s/n, Rio de Janeiro, Brazil
| | - Marcelo R Britto
- Museu Nacional, Universidade Federal do Rio de Janeiro, Quinta da Boa Vista s/n, Rio de Janeiro, Brazil
| | - Thaís de Assis Volpi
- Laboratório de Genética Animal, Programa de Pós-Graduação em Biologia Animal, Universidade Federal do Espírito Santo, Campus de Goiabeiras, Vitória, Brazil
| | - Mário C C de Pinna
- Museu de Zoologia da Universidade de São Paulo, 481 Av. Nazaré, São Paulo, São Paulo, 04263-000, Brazil
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Raposo MA, Kirwan GM, Lourenço ACC, Sobral G, Bockmann FA, Stopiglia R. On the notions of taxonomic ‘impediment’, ‘gap’, ‘inflation’ and ‘anarchy’, and their effects on the field of conservation. SYST BIODIVERS 2020. [DOI: 10.1080/14772000.2020.1829157] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Marcos A. Raposo
- Setor de Ornitologia, Departamento de Vertebrados, Museu Nacional, Universidade Federal do Rio de Janeiro, Quinta da Boa Vista, s/n, Rio de Janeiro, 20940–040, RJ, Brazil
- UMR 8590, IHPST–Institut d'Histoire et de Philosophie des Sciences et des Techniques, UMR 8590, Université Paris 1, Panthéon-Sorbonne & CNRS, 13 rue du Four, Paris, 75006, France
| | - Guy M. Kirwan
- Setor de Ornitologia, Departamento de Vertebrados, Museu Nacional, Universidade Federal do Rio de Janeiro, Quinta da Boa Vista, s/n, Rio de Janeiro, 20940–040, RJ, Brazil
| | - Ana Carolina Calijorne Lourenço
- Departamento de Ciências Biológicas, Universidade do Estado de Minas Gerais, Campus Ubá, Av. Olegário Maciel, 1427, Ubá, 36502-000, MG, Brazil
| | - Gisela Sobral
- Departamento de Reprodução Animal, Faculdade de Medicina Veterinária e Zootecnia, Universidade de São Paulo, Av. Prof. Dr. Orlando Marques de Paiva 87, São Paulo, 05508-270, SP, Brazil
| | - Flávio Alicino Bockmann
- Laboratório de Ictiologia de Ribeirão Preto, Departamento de Biologia, FFCLRP, Universidade de São Paulo, Av. dos Bandeirantes 3900, Ribeirão Preto, 14040–901, SP, Brazil
- Programa de Pós-Graduação em Biologia Comparada, FFCLRP, Universidade de São Paulo, Av. dos Bandeirantes 3900, Ribeirão Preto, Paris, 14040-901, SP, Brazil
| | - Renata Stopiglia
- Laboratório de Ictiologia de Ribeirão Preto, Departamento de Biologia, FFCLRP, Universidade de São Paulo, Av. dos Bandeirantes 3900, Ribeirão Preto, 14040–901, SP, Brazil
- Institut de Systématique, Évolution, Biodiversité, ISYEB, UMR 7205 – CNRS, MNHN, UPMC, EPHE, Muséum national d’Histoire naturelle, Sorbonne Universités, 57 rue Cuvier, CP 30, Paris, F-75005, France
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10
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Briñoccoli YF, Garrido GG, Alvarez A. DNA barcoding identifies three species of croakers (Pisces, Sciaenidae) in the ichthyoplankton of the High Paraná River. AN ACAD BRAS CIENC 2020; 92:e20180783. [PMID: 32428090 DOI: 10.1590/0001-3765202020180783] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2018] [Accepted: 11/21/2018] [Indexed: 08/30/2023] Open
Abstract
In the province of Misiones (Argentina), the filling of the Yacyretá Reservoir (Argentina-Paraguay) to its final dimensions in 2011 formed new aquatic ecosystem, e.g., Garupá Stream was converted into a subreservoir. Reports have been made in this stream of adult individuals and spawning of the Family Sciaenidae, excellent colonizers of modified environments. The larvae of this family are morphologically similar, particularly among Pachyurus and Plagioscion species, making taxonomic differentiation difficult. In the present work, sciaenidae larvae were characterized molecularly at the cytochrome c oxidase subunit I gene in order to determine which species use this environment for reproduction. Additionally, genetic distances, Barcode Index Number (BIN) and Automatic Barcode Gap Discovery method (ABGD) were estimated and phylogenetic trees were reconstructed. The results indicated the presence of Plagioscion ternetzi and Pachyurus bonariensis larvae, and for the first time in tributaries of the region, Plagioscion squamosissimus. The incorporation of P. bonariensis and P. squamosissimus to the faunistic assemblage of ichthyoplankton in the Garupá Stream supports better characterization of the species richness of this secondary watercourse modified by the Yacyretá Reservoir, and advancement in our understanding of use of this area for reproduction.
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Affiliation(s)
- Yanina F Briñoccoli
- Departamento de Biología, Universidad Nacional de Misiones, Posadas, Misiones, Argentina
| | - Gladys G Garrido
- CONICET-UNaM, Instituto de Biología Subtropical Nodo Posadas, Posadas, Misiones, Argentina
| | - Alicia Alvarez
- CONICET-UNaM, Instituto de Biología Subtropical Nodo Posadas, Posadas, Misiones, Argentina
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Limmon G, Delrieu-Trottin E, Patikawa J, Rijoly F, Dahruddin H, Busson F, Steinke D, Hubert N. Assessing species diversity of Coral Triangle artisanal fisheries: A DNA barcode reference library for the shore fishes retailed at Ambon harbor (Indonesia). Ecol Evol 2020; 10:3356-3366. [PMID: 32273993 PMCID: PMC7141007 DOI: 10.1002/ece3.6128] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2019] [Revised: 01/30/2020] [Accepted: 02/03/2020] [Indexed: 01/01/2023] Open
Abstract
The Coral Triangle (CT), a region spanning across Indonesia and Philippines, is home to about 4,350 marine fish species and is among the world's most emblematic regions in terms of conservation. Threatened by overfishing and oceans warming, the CT fisheries have faced drastic declines over the last decades. Usually monitored through a biomass-based approach, fisheries trends have rarely been characterized at the species level due to the high number of taxa involved and the difficulty to accurately and routinely identify individuals to the species level. Biomass, however, is a poor proxy of species richness, and automated methods of species identification are required to move beyond biomass-based approaches. Recent meta-analyses have demonstrated that species richness peaks at intermediary levels of biomass. Consequently, preserving biomass is not equal to preserving biodiversity. We present the results of a survey to estimate the shore fish diversity retailed at the harbor of Ambon Island, an island located at the center of the CT that display exceptionally high biomass despite high levels of threat, while building a DNA barcode reference library of CT shore fishes targeted by artisanal fisheries. We sampled 1,187 specimens and successfully barcoded 696 of the 760 selected specimens that represent 202 species. Our results show that DNA barcodes were effective in capturing species boundaries for 96% of the species examined, which opens new perspectives for the routine monitoring of the CT fisheries.
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Affiliation(s)
- Gino Limmon
- Pusat Kemaritiman dan Kelautan Universitas Pattimura (Maritime and Marine Science Center of Excellence) Ambon Indonesia
| | - Erwan Delrieu-Trottin
- Institut de Recherche pour le Développement UMR 226 ISEM (UM-CNRS-IRD-EPHE) Montpellier France
- Museum für Naturkunde Leibniz-Institut für Evolutions-und Biodiversitätsforschung an der Humboldt-Universität zu Berlin Berlin Germany
| | - Jesaya Patikawa
- Pusat Kemaritiman dan Kelautan Universitas Pattimura (Maritime and Marine Science Center of Excellence) Ambon Indonesia
| | - Frederik Rijoly
- Pusat Kemaritiman dan Kelautan Universitas Pattimura (Maritime and Marine Science Center of Excellence) Ambon Indonesia
| | - Hadi Dahruddin
- Division of Zoology Research Center for Biology Indonesian Institute of Sciences (LIPI) Cibinong Indonesia
| | - Frédéric Busson
- Institut de Recherche pour le Développement UMR 226 ISEM (UM-CNRS-IRD-EPHE) Montpellier France
- UMR 7208 BOREA (MNHN-CNRS-UPMC-IRD-UCBN) Muséum National d'Histoire Naturelle Paris France
| | - Dirk Steinke
- Department of Integrative Biology Centre for Biodiversity Genomics University of Guelph Guelph ON Canada
| | - Nicolas Hubert
- Institut de Recherche pour le Développement UMR 226 ISEM (UM-CNRS-IRD-EPHE) Montpellier France
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Back from the Past: DNA Barcodes and Morphology Support Ablabesmyia americana Fittkau as a Valid Species (Diptera: Chironomidae). DIVERSITY 2019. [DOI: 10.3390/d11090173] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Short, standardized gene fragments for species identification (DNA barcodes) have proven effective in delineating closely-related insect species, and can be critical characters to include in taxonomic studies. This is also the case for the species-rich and widely distributed fly family Chironomidae (non-biting midges). Inspired by observed genetic differences in partial COI gene sequences between North American and European populations of the chironomid Ablabesmyia monilis sensu lato, we investigated whether or not the morphology of male and female adults supported the distinction of more than one species. Our results support that the junior synonym Ablabesmyia americana is a valid species separate from A. monilis, and that A. monilis sensu stricto is distributed both in the Palearctic region and in North America. We provide re-descriptions of all of the major life stages of A. americana and of the adult female of A. monilis.
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Sun CH, Liu DW, Huang YL, Zhou YW, Hou SL, Lu CH. Genetic diversity analysis of Peking gecko ( Gekko swinhonis) in mid-Eastern China based on mitochondrial COI and Cyt b gene sequences. MITOCHONDRIAL DNA PART B-RESOURCES 2019; 4:2156-2158. [PMID: 33365452 PMCID: PMC7687432 DOI: 10.1080/23802359.2019.1623724] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
To understand the genetic diversity of Peking gecko (Gekko swinhonis) populations in its endemic region, 60 individuals were sampled from Lushan, Qi, and Linying counties in Henan Province, China. Through PCR amplification and Sanger sequencing, 120 sequences with lengths of 652 bp (COI) and 739 bp (Cyt b) were obtained, and nine haplotypes were detected for each gene. Overall, results indicated that Peking gecko populations in China have high genetic diversity and significant genetic differentiation. This study provides necessary scientific basis for the protection of Peking gecko germplasm resources.
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Affiliation(s)
- Cheng-He Sun
- College of Biology and the Environment, Nanjing Forestry University, Nanjing, China
| | - Da-Wei Liu
- Forest Police Identification Center of National Forestry Administration, Nanjing Forest Police College, Nanjing, China
| | - Ya-Lin Huang
- Forest Police Identification Center of National Forestry Administration, Nanjing Forest Police College, Nanjing, China
| | - Yong-Wu Zhou
- Forest Police Identification Center of National Forestry Administration, Nanjing Forest Police College, Nanjing, China
| | - Sen-Lin Hou
- Forest Police Identification Center of National Forestry Administration, Nanjing Forest Police College, Nanjing, China
| | - Chang-Hu Lu
- College of Biology and the Environment, Nanjing Forestry University, Nanjing, China
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14
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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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15
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Shen Y, Hubert N, Huang Y, Wang X, Gan X, Peng Z, He S. DNA barcoding the ichthyofauna of the Yangtze River: Insights from the molecular inventory of a mega‐diverse temperate fauna. Mol Ecol Resour 2019; 19:1278-1291. [DOI: 10.1111/1755-0998.12961] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2018] [Revised: 09/07/2018] [Accepted: 09/24/2018] [Indexed: 01/04/2023]
Affiliation(s)
- Yanjun Shen
- The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology Chinese Academy of Sciences Wuhan China
- University of Chinese Academy of Sciences Beijing China
| | - Nicolas Hubert
- Institut de Recherche pour le Développement UMR 226 ISEM (UM2‐CNRS‐IRD) Montpellier cedex 05 France
| | - Yan Huang
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education) Southwest University School of Life Sciences Chongqing China
| | - Xuzheng Wang
- The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology Chinese Academy of Sciences Wuhan China
| | - Xiaoni Gan
- The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology Chinese Academy of Sciences Wuhan China
| | - Zuogang Peng
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education) Southwest University School of Life Sciences Chongqing China
| | - Shunping He
- The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology Chinese Academy of Sciences Wuhan China
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16
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García-Melo JE, Oliveira C, Da Costa Silva GJ, Ochoa-Orrego LE, Garcia Pereira LH, Maldonado-Ocampo JA. Species delimitation of neotropical Characins (Stevardiinae): Implications for taxonomy of complex groups. PLoS One 2019; 14:e0216786. [PMID: 31166941 PMCID: PMC6550444 DOI: 10.1371/journal.pone.0216786] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2018] [Accepted: 04/29/2019] [Indexed: 12/21/2022] Open
Abstract
Accurate species delimitation is crucial for studies of phylogeny, phylogeography, ecology, conservation and biogeography. The limits of species and genera in the Characidae family are controversial due to its uncertain phylogenetic relationships, high level of morphological homoplasy and the use of ambiguous morphological characters for descriptions. Here we establish species boundaries for Bryconamericus, Hemibrycon, Knodus and Eretmobrycon (Stevardiinae: Characidae), previously diagnosed with morphology, using three different barcoding approaches (GMYC, PTP, ABGD). Results revealed that species delimitation was successful by the use of a single-gene approach and by following a workflow in the context of integrative taxonomy, making evident problems and mistakes in the cataloging of Characidae species. Hence, it was possible to infer boundaries at genus level for clusters in the trees (GMYC and PTP) and automatic partitions (ABGD) which were consistent with some of recent taxonomic changes proposed in Characidae. We found that discordance cases between methods were linked to limitations of the methods and associated to putative species cluster closely related, some historically problematic in their diagnosis and identification. Furthermore, we suggested taxonomic changes and possibly new species, revealing a high degree of hidden diversity. Finally, we propose a workflow as a fast, accurate and objective way to delimit species from mitochondrial DNA sequences and to help clarify the classification of this group.
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Affiliation(s)
- Jorge E. García-Melo
- Laboratorio de Ictiología, Unidad de Ecología y Sistemática (UNESIS), Departamento de Biología, Facultad de Ciencias, Pontificia Universidad Javeriana, Bogotá, Colombia
| | - Claudio Oliveira
- Departamento de Morfologia, Instituto de Biociências, Universidade Estadual Paulista (UNESP), Campus de Botucatu, Botucatu, SP, Brazil
| | - Guilherme José Da Costa Silva
- Departamento de Morfologia, Instituto de Biociências, Universidade Estadual Paulista (UNESP), Campus de Botucatu, Botucatu, SP, Brazil
- Universidade Santo Amaro, Rua Prof. Enéas de Siqueira Neto, Jardim das Imbuias, São Paulo—SP, Brazil
| | - Luz E. Ochoa-Orrego
- Departamento de Morfologia, Instituto de Biociências, Universidade Estadual Paulista (UNESP), Campus de Botucatu, Botucatu, SP, Brazil
| | - Luiz Henrique Garcia Pereira
- Centro de Ciências da Vida e da Natureza, Universidade Federal da Integração Latino-Americana–UNILA, Foz do Iguaçu, Paraná, Brazil
| | - Javier A. Maldonado-Ocampo
- Laboratorio de Ictiología, Unidad de Ecología y Sistemática (UNESIS), Departamento de Biología, Facultad de Ciencias, Pontificia Universidad Javeriana, Bogotá, Colombia
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17
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Sonet G, Snoeks J, Nagy ZT, Vreven E, Boden G, Breman FC, Decru E, Hanssens M, Ibala Zamba A, Jordaens K, Mamonekene V, Musschoot T, Van Houdt J, Van Steenberge M, Lunkayilakio Wamuini S, Verheyen E. DNA barcoding fishes from the Congo and the Lower Guinean provinces: Assembling a reference library for poorly inventoried fauna. Mol Ecol Resour 2019; 19:728-743. [DOI: 10.1111/1755-0998.12983] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2018] [Revised: 11/03/2018] [Accepted: 11/27/2018] [Indexed: 11/28/2022]
Affiliation(s)
- Gontran Sonet
- OD Taxonomy and Phylogeny ‐ JEMU Royal Belgian Institute of Natural Sciences Brussels Belgium
| | - Jos Snoeks
- Department of Biology – Vertebrates, Entomology, JEMU Royal Museum for Central Africa Tervuren Belgium
- Laboratory of Biodiversity and Evolutionary Genomics KU Leuven Leuven Belgium
| | - Zoltán T. Nagy
- OD Taxonomy and Phylogeny ‐ JEMU Royal Belgian Institute of Natural Sciences Brussels Belgium
| | - Emmanuel Vreven
- Department of Biology – Vertebrates, Entomology, JEMU Royal Museum for Central Africa Tervuren Belgium
| | - Gert Boden
- Department of Biology – Vertebrates, Entomology, JEMU Royal Museum for Central Africa Tervuren Belgium
| | - Floris C. Breman
- Department of Biology – Vertebrates, Entomology, JEMU Royal Museum for Central Africa Tervuren Belgium
- Research, Biosystematics Group Wageningen University Wageningen The Netherlands
| | - Eva Decru
- Department of Biology – Vertebrates, Entomology, JEMU Royal Museum for Central Africa Tervuren Belgium
| | - Mark Hanssens
- Department of Biology – Vertebrates, Entomology, JEMU Royal Museum for Central Africa Tervuren Belgium
| | - Armel Ibala Zamba
- Institut de Développement Rural Université Marien Ngouabi Brazzaville Republic of the Congo
| | - Kurt Jordaens
- Department of Biology – Vertebrates, Entomology, JEMU Royal Museum for Central Africa Tervuren Belgium
- Department of Biology ‐ Evolutionary Ecology Group University of Antwerp Antwerp Belgium
| | - Victor Mamonekene
- Institut de Développement Rural Université Marien Ngouabi Brazzaville Republic of the Congo
| | - Tobias Musschoot
- Department of Biology – Vertebrates, Entomology, JEMU Royal Museum for Central Africa Tervuren Belgium
| | | | - Maarten Van Steenberge
- OD Taxonomy and Phylogeny ‐ JEMU Royal Belgian Institute of Natural Sciences Brussels Belgium
- Department of Biology – Vertebrates, Entomology, JEMU Royal Museum for Central Africa Tervuren Belgium
- Laboratory of Biodiversity and Evolutionary Genomics KU Leuven Leuven Belgium
| | - Soleil Lunkayilakio Wamuini
- Département de Biologie I. S. P. Mbanza‐Ngungu Mbanza‐Ngungu Democratic Republic of the Congo
- Functional and Evolutionary Morphology Laboratory University of Liège Liège Belgium
| | - Erik Verheyen
- OD Taxonomy and Phylogeny ‐ JEMU Royal Belgian Institute of Natural Sciences Brussels Belgium
- Department of Biology ‐ Evolutionary Ecology Group University of Antwerp Antwerp Belgium
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18
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Jennings WB, Ruschi PA, Ferraro G, Quijada CC, Silva-Malanski ACG, Prosdocimi F, Buckup PA. Barcoding the Neotropical freshwater fish fauna using a new pair of universal COI primers with a discussion of primer dimers and M13 primer tails. Genome 2019; 62:77-83. [PMID: 30730769 DOI: 10.1139/gen-2018-0145] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Designing primers for DNA barcoding is a significant challenge for the rich Neotropical fish fauna, which is comprised of ∼6000 species. Previously, researchers required multiple pairs of PCR primers or primer cocktails to obtain standard COI (i.e., mitochondrial cytochrome c oxidase subunit I) barcode sequences from assemblages of freshwater fish in this region. To simplify DNA barcoding and metabarcoding studies of Neotropical freshwater fish, we present a new pair of COI primers, which have yielded high quality barcodes across six teleost orders-Characiformes, Cichliformes, Cyprinodontiformes, Gymnotiformes, Siluriformes, and Synbranchiformes-native to South America. Following previous fish barcoding studies, we also tailed our primers with M13 forward and reverse primers to facilitate the DNA sequencing process. Although this practice generates primer dimers, we obtained complete and high quality COI barcode sequences for all samples. We discuss the problem of primer dimers and suggest strategies for neutralizing their influence on data quality.
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Affiliation(s)
- W Bryan Jennings
- a Departamento de Vertebrados, Museu Nacional, Universidade Federal do Rio de Janeiro, Quinta da Boa Vista, 20940-040 Rio de Janeiro, RJ, Brazil
| | - Piero A Ruschi
- a Departamento de Vertebrados, Museu Nacional, Universidade Federal do Rio de Janeiro, Quinta da Boa Vista, 20940-040 Rio de Janeiro, RJ, Brazil
| | - Gustavo Ferraro
- a Departamento de Vertebrados, Museu Nacional, Universidade Federal do Rio de Janeiro, Quinta da Boa Vista, 20940-040 Rio de Janeiro, RJ, Brazil
| | - Carla Christie Quijada
- a Departamento de Vertebrados, Museu Nacional, Universidade Federal do Rio de Janeiro, Quinta da Boa Vista, 20940-040 Rio de Janeiro, RJ, Brazil
| | - Ana Cecilia Gomes Silva-Malanski
- a Departamento de Vertebrados, Museu Nacional, Universidade Federal do Rio de Janeiro, Quinta da Boa Vista, 20940-040 Rio de Janeiro, RJ, Brazil
| | - Francisco Prosdocimi
- b Laboratório de Genômica e Biodiversidade, Instituto de Bioquímica Médica Leopoldo de Meis, Universidade Federal do Rio de Janeiro, 21941-902, Rio de Janeiro, RJ, Brazil
| | - Paulo A Buckup
- a Departamento de Vertebrados, Museu Nacional, Universidade Federal do Rio de Janeiro, Quinta da Boa Vista, 20940-040 Rio de Janeiro, RJ, Brazil
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19
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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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20
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Sales NG, Mariani S, Salvador GN, Pessali TC, Carvalho DC. Hidden Diversity Hampers Conservation Efforts in a Highly Impacted Neotropical River System. Front Genet 2018; 9:271. [PMID: 30087693 PMCID: PMC6066647 DOI: 10.3389/fgene.2018.00271] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2017] [Accepted: 07/03/2018] [Indexed: 11/13/2022] Open
Abstract
Neotropical Rivers host a highly diverse ichthyofauna, but taxonomic uncertainty prevents appropriate conservation measures. The Doce River Basin (DRB), lying within two Brazilian threatened hotspots (Atlantic Forest and Brazilian Savanna) in south-east Brazil, faced the worst ever environmental accident reported for South American catchments, due to a dam collapse that spread toxic mining tailings along the course of its main river. Its ichthyofauna was known to comprise 71 native freshwater fish species, of which 13 endemic. Here, we build a DNA barcode library for the DRB ichthyofauna, using samples obtained before the 2015 mining disaster, in order to provide a more robust biodiversity record for this basin, as a baseline for future management actions. Throughout the whole DRB, we obtained a total of 306 barcodes, assigned to 69 putative species (with a mean of 4.54 barcodes per species), belonging to 45 genera, 18 families, and 5 orders. Average genetic distances within species, genus, and families were 2.59, 11.4, and 20.5%, respectively. The 69 species identified represent over 76% of the known DRB ichthyofauna, comprising 43 native (five endemic, of which three threatened by extinction), 13 already known introduced species, and 13 unknown species (such as Characidium sp., Neoplecostomus sp., and specimens identified only at the sub-family level Neoplecostominae, according to morphological identification provided by the museum collections). Over one fifth of all analyzed species (N = 16) had a mean intraspecific genetic divergence higher than 2%. An integrative approach, combining NND (nearest neighbor distance), BIN (barcode index number), ABGD (automatic barcode gap discovery), and bPTP (Bayesian Poisson Tree Processes model) analyses, suggested the occurrence of potential cryptic species, species complex, or historical errors in morphological identification. The evidence presented calls for a more robust, DNA-assisted cataloging of biodiversity-rich ecosystems, in order to enable effective monitoring and informed actions to preserve and restore these delicate habitats.
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Affiliation(s)
- Naiara G Sales
- Ecosystems and Environment Research Centre, School of Environment & Life Sciences, University of Salford, Salford, United Kingdom
| | - Stefano Mariani
- Ecosystems and Environment Research Centre, School of Environment & Life Sciences, University of Salford, Salford, United Kingdom
| | - Gilberto N Salvador
- Laboratório de Ecologia e Conservação, Universidade Federal do Pará, Belém, Brazil
| | - Tiago C Pessali
- Museu de Ciências Naturais PUC Minas, Pontifícia Universidade Católica de Minas Gerais, Belo Horizonte, Brazil
| | - Daniel C Carvalho
- Programa de Pós-graduação em Biologia de Vertebrados, Pontifícia Universidade Católica de Minas Gerais, Belo Horizonte, Brazil
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21
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Souza-Shibatta L, Tonini JFR, Abrahão VP, Jarduli LR, Oliveira C, Malabarba LR, Sofia SH, Shibatta OA. Reappraisal of the systematics of Microglanis cottoides (Siluriformes, Pseudopimelodidae), a catfish from southern Brazil. PLoS One 2018; 13:e0199963. [PMID: 29975765 PMCID: PMC6033443 DOI: 10.1371/journal.pone.0199963] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2018] [Accepted: 06/18/2018] [Indexed: 11/23/2022] Open
Abstract
The southern region of Brazil is characterized by high species diversity and endemism of freshwater fishes distributed across geographically isolated river basins. Microglanis cottoides has a widespread range across these river basins and occurs in sympatry with other endemic species of the genus (e.g. M. cibelae, M. eurystoma, and M. malabarbai). Herein we tested the monophyly of M. cottoides and presented for the first time information about the molecular phylogeny of species in the genus. The results suggest that M. cottoides currently forms a non-monophyletic group which includes populations endemic to the Uruguay River basin that are more closely related to M. malabarbai, and excludes M. cibelae, found to be nested within M. cottoides. Based on an integrative approach using morphological and molecular data, we propose M. cibelae as a junior synonym of M. cottoides, and the populations of the Uruguay River basin previously assigned to M. cottoides in fact belong to M. malabarbai. Our molecular phylogeny shows that M. cottoides is sister to M. parahybae, which is also a coastal species, and M. malabarbai is sister of M. garavelloi, both endemic to inland river basins. The time-calibrated phylogeny indicates that the separation between inland and the coastal clades occurred in the Tertiary period, and that the species within the coastal basins diverged in the Pliocene, which overlaps with the diversification times estimated for the two inland species as well. This pattern of diversification corroborates some previous studies with other fishes from the same region.
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Affiliation(s)
- Lenice Souza-Shibatta
- Laboratório de Genética e Ecologia Animal, Departamento de Biologia Geral, Universidade Estadual de Londrina, Londrina, PR, Brazil
| | - João F. R. Tonini
- Department of Organismic and Evolutionary Biology, Museum of Comparative Zoology, Harvard University, Cambridge, MA, United States of America
| | - Vitor P. Abrahão
- Universidade de São Paulo, Museu de Zoologia da USP, São Paulo, SP, Brasil
| | | | - Claudio Oliveira
- Laboratório de Biologia e Genética de Peixes, Departamento de Morfologia, Instituto de Biociências, Universidade Estadual Paulista -UNESP, Botucatu, SP, Brazil
| | - Luiz R. Malabarba
- Departamento de Zoologia, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil
| | - Silvia H. Sofia
- Laboratório de Genética e Ecologia Animal, Departamento de Biologia Geral, Universidade Estadual de Londrina, Londrina, PR, Brazil
| | - Oscar A. Shibatta
- Departamento de Biologia Animal e Vegetal, Universidade Estadual de Londrina, Londrina, PR, Brazil
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22
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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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23
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Morais-Silva JP, Oliveira AVD, Fabrin TMC, Diamante NA, Prioli SMAP, Frota A, Graça WJD, Prioli AJ. Geomorphology Influencing the Diversification of Fish in Small-Order Rivers of Neighboring Basins. Zebrafish 2018; 15:389-397. [PMID: 29653071 DOI: 10.1089/zeb.2017.1551] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
The current analysis investigates whether the uplift of the Serra da Esperança and the Ponta Grossa Arch in the Serra Geral resulted in ichthyofaunistic changes in adjacent basins. For this, we describe the phylogeographic structure among populations of Trichomycterus collected in hydrographic basins in southern Brazil by using partial nucleotide sequences of the mitochondrial gene Cytochrome C Oxidase subunit I. Analyses revealed that the nomenclature Trichomycterus davisi fails to contain the whole genetic diversity range found in the collected specimens and indicates at least six genetic lineages in Trichomycterus. Diagnostic morphological characteristics not associated to T. davisi could be identified in some specimens from the Iguaçu Piquiri haplogroup, indicating the occurrence of species Trichomycterus stawiarski. The lack of morphological differences among the other clades clearly suggests a cryptic species case. Molecular analyses revealed at least five new species besides T. davisi in the hydrographic basins and support the interpretation that genetic structure in T. davisi species complex is explained by tectonic events intrinsic to the areas of influence of Serra da Esperança and the Ponta Grossa Arch which occurred around 1.7 My.
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Affiliation(s)
- João P Morais-Silva
- 1 Programa de Pós-graduação em Biologia Comparada, Universidade Estadual de Maringá , Maringá, Brazil
| | - Alessandra V de Oliveira
- 2 Departamento de Biotecnologia, Genética e Biologia Celular, Universidade Estadual de Maringá , Maringá, Brazil .,3 Núcleo de Pesquisas em Limnologia, Ictiologia e Aquicultura (Nupélia), Universidade Estadual de Maringá , Maringá, Brazil
| | - Thomaz M C Fabrin
- 4 Programa de Pós-graduação em Ecologia de Ambientes Aquáticos Continentais, Universidade Estadual de Maringá , Maringá, Brazil
| | - Nathália Alves Diamante
- 1 Programa de Pós-graduação em Biologia Comparada, Universidade Estadual de Maringá , Maringá, Brazil
| | - Sônia M A P Prioli
- 2 Departamento de Biotecnologia, Genética e Biologia Celular, Universidade Estadual de Maringá , Maringá, Brazil .,3 Núcleo de Pesquisas em Limnologia, Ictiologia e Aquicultura (Nupélia), Universidade Estadual de Maringá , Maringá, Brazil
| | - Augusto Frota
- 4 Programa de Pós-graduação em Ecologia de Ambientes Aquáticos Continentais, Universidade Estadual de Maringá , Maringá, Brazil
| | - Weferson J da Graça
- 3 Núcleo de Pesquisas em Limnologia, Ictiologia e Aquicultura (Nupélia), Universidade Estadual de Maringá , Maringá, Brazil .,5 Departamento de Biologia, Universidade Estadual de Maringá , Maringá, Brazil
| | - Alberto J Prioli
- 3 Núcleo de Pesquisas em Limnologia, Ictiologia e Aquicultura (Nupélia), Universidade Estadual de Maringá , Maringá, Brazil
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Souza CS, Costa-Silva GJ, Roxo FF, Foresti F, Oliveira C. Genetic and Morphological Analyses Demonstrate That Schizolecis guntheri (Siluriformes: Loricariidae) Is Likely to Be a Species Complex. Front Genet 2018; 9:69. [PMID: 29552028 PMCID: PMC5841391 DOI: 10.3389/fgene.2018.00069] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2017] [Accepted: 02/15/2018] [Indexed: 01/16/2023] Open
Abstract
Schizolecis is a monotypic genus of Siluriformes widely distributed throughout isolated coastal drainages of southeastern Brazil. Previous studies have shown that fish groups found in isolated river basins tend to differentiate over time in the absence of gene flow, resulting in allopatric speciation. In this study, we used partial sequences of the mitochondrial gene COI with the analysis of the General Mixed Yule Coalescent model (GMYC) and the Automatic Barcode Gap Discovery (ABGD) for single locus species delimitation, and a Principal Component Analysis (PCA) of external morphology to test the hypothesis that Schizolecis guntheri is a complex of species. We analyzed 94 samples of S. guntheri for GMYC and ABGD, and 82 samples for PCA from 22 coastal rivers draining to the Atlantic in southeastern Brazil from the Paraná State to the north of the Rio de Janeiro State. As a result, the GMYC model and the ABGD delimited five operational taxonomy units (OTUs – a nomenclature referred to in the present study of the possible new species delimited for the genetic analysis), a much higher number compared to the traditional alfa taxonomy that only recognizes S. guntheri across the isolated coastal rivers of Brazil. Furthermore, the PCA analysis suggests that S. guntheri is highly variable in aspects of external body proportions, including dorsal-fin spine length, pectoral-fin spine length, pelvic-fin spine length, lower caudal-fin spine length, caudal peduncle depth, anal width and mandibular ramus length. However, no exclusive character was found among the isolated populations that could be used to describe a new species of Schizolecis. Therefore, we can conclude, based on our results of PCA contrasting with the results of GMYC and ABGD, that S. guntheri represents a complex of species.
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Affiliation(s)
- Camila S Souza
- Departamento de Morfologia, Universidade Estadual Paulista "Júlio de Mesquita Filho", Instituto de Biociências de Botucatu, Botucatu, Brazil
| | - Guilherme J Costa-Silva
- Departamento de Morfologia, Universidade Estadual Paulista "Júlio de Mesquita Filho", Instituto de Biociências de Botucatu, Botucatu, Brazil.,Departamento de Biologia, Universidade Santo Amaro, São Paulo, Brazil
| | - Fábio F Roxo
- Departamento de Morfologia, Universidade Estadual Paulista "Júlio de Mesquita Filho", Instituto de Biociências de Botucatu, Botucatu, Brazil
| | - Fausto Foresti
- Departamento de Morfologia, Universidade Estadual Paulista "Júlio de Mesquita Filho", Instituto de Biociências de Botucatu, Botucatu, Brazil
| | - Claudio Oliveira
- Departamento de Morfologia, Universidade Estadual Paulista "Júlio de Mesquita Filho", Instituto de Biociências de Botucatu, Botucatu, Brazil
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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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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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Birindelli JLO, Sidlauskas BL. Preface: How far has Neotropical Ichthyology progressed in twenty years? NEOTROPICAL ICHTHYOLOGY 2018. [DOI: 10.1590/1982-0224-20180128] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
ABSTRACT Studies on the diversity, taxonomy, phylogeny, and biogeography of Neotropical Fishes have thrived over the twenty years that have elapsed since the first symposium on their phylogeny and classification in Porto Alegre, Brazil. Here, we review recent advances in the study of Neotropical fishes and assess the known diversity of freshwater species in that region. 6,255 valid freshwater species have been discovered in the Neotropics so far, and we estimate that over 9,000 species will be known when the inventory is complete. We also summarize the events of the second Symposium on Phylogeny and Classification of Neotropical Fishes that took place last year in Londrina, Brazil. Along with invited talks on the biodiversity of all major groups of Neotropical fishes, a series of presentations on the development of fish collections, and numerous contributed talks, the meeting included a special session to honor Dr. Richard Vari, who was one of the most prolific and beloved members of our community.
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Prizon AC, Bruschi DP, Borin-Carvalho LA, Cius A, Barbosa LM, Ruiz HB, Zawadzki CH, Fenocchio AS, Portela-Castro ALDB. Hidden Diversity in the Populations of the Armored Catfish Ancistrus Kner, 1854 (Loricariidae, Hypostominae) from the Paraná River Basin Revealed by Molecular and Cytogenetic Data. Front Genet 2017; 8:185. [PMID: 29225612 PMCID: PMC5705632 DOI: 10.3389/fgene.2017.00185] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2017] [Accepted: 11/07/2017] [Indexed: 12/01/2022] Open
Abstract
Only one species of armored catfish, Ancistrus cirrhosus Valenciennes 1836, has been historically described in the basin of the Paraná River, from Misiones (Argentina). However, the ample variation found in the morphology and coloration of the populations sampled in the tributaries of the Brazilian state of Paraná makes it difficult to establish the real taxonomic status and evolutionary history of the Ancistrus specimens, suggesting that A. cirrhosus is not the only species found in this basin. By combining data on mitochondrial DNA (COI gene) and chromosomal markers from different Ancistrus populations, totaling 144 specimens, in the tributaries of the Paraná, and specimens from Misiones (type-locality of A. cirrhosus), we detected five distinct evolutionary lineages. All the specimens were 2n = 50, but had four distinct karyotype formulae. The results of the Generalized Mixed Yule Coalescent (GYMC) and the genetic distances (uncorrected P-values) between lineages ranged from 3 to 5%. Clusters of 18S rDNA were observed in a single chromosome pair in seven populations of Ancistrus, but at different positions, in some cases, in synteny with the 5S rDNA sites. Multiple 5S sites were observed in all populations. Overall, the cytogenetic data reinforce the genetic evidence of the diversification of lineages, and indicate the existence of candidate species in the study region. The evidence indicates that at least four candidate species of the Ancistrus may coexist in the Paraná basin besides A. cirrhosus. Overall, our results provide a comprehensive scenario for the genetic variation among Ancistrus populations and reinforce the conclusion that the true diversity of the freshwater fish of the Neotropical regions has been underestimated.
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Affiliation(s)
- Ana C Prizon
- Laboratório de Citogenética de Vertebrados, Departamento de Biotecnologia, Genética e Biologia Celular, Universidade Estadual de Maringá, Maringá, Brazil
| | - Daniel P Bruschi
- Laboratório de Citogenética Animal e Mutagênese Ambioental, Departamento de Genética, Universidade Federal do Paraná, Curitiba, Brazil
| | - Luciana A Borin-Carvalho
- Laboratório de Citogenética de Vertebrados, Departamento de Biotecnologia, Genética e Biologia Celular, Universidade Estadual de Maringá, Maringá, Brazil
| | - Andréa Cius
- Laboratório de Citogenética de Vertebrados, Departamento de Biotecnologia, Genética e Biologia Celular, Universidade Estadual de Maringá, Maringá, Brazil
| | - Ligia M Barbosa
- Laboratório de Citogenética de Vertebrados, Departamento de Biotecnologia, Genética e Biologia Celular, Universidade Estadual de Maringá, Maringá, Brazil
| | - Henrique B Ruiz
- Departamento de Biologia/Nupélia, Universidade Estadual de Maringá, Maringá, Brazil
| | - Claudio H Zawadzki
- Departamento de Biologia/Nupélia, Universidade Estadual de Maringá, Maringá, Brazil
| | - Alberto S Fenocchio
- Facultad de Ciencias Exactas, Químicas y Naturales, Universidad Nacional de Misiones, Posadas, Argentina
| | - Ana L de Brito Portela-Castro
- Laboratório de Citogenética de Vertebrados, Departamento de Biotecnologia, Genética e Biologia Celular, Universidade Estadual de Maringá, Maringá, Brazil
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Employing DNA barcoding as taxonomy and conservation tools for fish species censuses at the southeastern Mediterranean, a hot-spot area for biological invasion. J Nat Conserv 2017. [DOI: 10.1016/j.jnc.2017.01.004] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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30
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Santos ARD, Usso MC, Gouveia JG, Araya-Jaime C, Frantine-Silva W, Giuliano-Caetano L, Foresti F, Dias AL. Chromosomal Mapping of Repetitive DNA Sequences in the Genus Bryconamericus (Characidae) and DNA Barcoding to Differentiate Populations. Zebrafish 2017; 14:261-271. [PMID: 28355106 DOI: 10.1089/zeb.2016.1380] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The mapping of repetitive DNA sites by fluorescence in situ hybridization has been widely used for karyotype studies in different species of fish, especially when dealing with related species or even genera presenting high chromosome variability. This study analyzed three populations of Bryconamericus, with diploid number preserved, but with different karyotype formulae. Bryconamericus ecai, from the Forquetinha river/RS, presented three new cytotypes, increasing the number of karyotype forms to seven in this population. Other two populations of Bryconamericus sp. from the Vermelho stream/PR and Cambuta river/PR exhibited interpopulation variation. The chromosome mapping of rDNA sites revealed unique markings among the three populations, showing inter- and intrapopulation variability located in the terminal region. The molecular analysis using DNA barcoding complementing the cytogenetic analysis also showed differentiation among the three populations. The U2 small nuclear DNA repetitive sequence exhibited conserved features, being located in the interstitial region of a single chromosome pair. This is the first report on its occurrence in the genus Bryconamericus. Data obtained revealed a karyotype variability already assigned to the genus, along with polymorphism of ribosomal sites, demonstrating that this group of fish can be undergoing a divergent evolutionary process, constituting a substantive model for studies of chromosomal evolution.
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Affiliation(s)
- Angélica Rossotti Dos Santos
- 1 Laboratório de Citogenética Animal, Departamento de Biologia Geral, Universidade Estadual de Londrina , Londrina, Brazil
| | - Mariana Campaner Usso
- 1 Laboratório de Citogenética Animal, Departamento de Biologia Geral, Universidade Estadual de Londrina , Londrina, Brazil
| | - Juceli Gonzalez Gouveia
- 1 Laboratório de Citogenética Animal, Departamento de Biologia Geral, Universidade Estadual de Londrina , Londrina, Brazil
| | - Cristian Araya-Jaime
- 2 Laboratório de Citogenética de Vertebrados, ICBM Facultad de Medicina, Universidad de Chile , Santiago, Chile .,3 Laboratório de Genética e Ecologia Animal, Departamento de Biologia Geral, Universidade Estadual de Londrina , Londrina, Brazil .,4 Departamento de Morfologia, Instituto de Biociências, Universidade Estadual Paulista , Botucatu, Brazil
| | - Wilson Frantine-Silva
- 3 Laboratório de Genética e Ecologia Animal, Departamento de Biologia Geral, Universidade Estadual de Londrina , Londrina, Brazil
| | - Lucia Giuliano-Caetano
- 1 Laboratório de Citogenética Animal, Departamento de Biologia Geral, Universidade Estadual de Londrina , Londrina, Brazil
| | - Fausto Foresti
- 4 Departamento de Morfologia, Instituto de Biociências, Universidade Estadual Paulista , Botucatu, Brazil
| | - Ana Lúcia Dias
- 1 Laboratório de Citogenética Animal, Departamento de Biologia Geral, Universidade Estadual de Londrina , Londrina, Brazil
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Pazza R, Cruvinel LA, Kavalco KF. Parallel evolution evidenced by molecular data in the banded-tetra (Astyanax fasciatus). BIOCHEM SYST ECOL 2017. [DOI: 10.1016/j.bse.2016.10.024] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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Rossini BC, Oliveira CAM, de Melo FAG, Bertaco VDA, de Astarloa JMD, Rosso JJ, Foresti F, Oliveira C. Highlighting Astyanax Species Diversity through DNA Barcoding. PLoS One 2016; 11:e0167203. [PMID: 27992537 PMCID: PMC5167228 DOI: 10.1371/journal.pone.0167203] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2016] [Accepted: 11/10/2016] [Indexed: 11/18/2022] Open
Abstract
DNA barcoding has been used extensively to solve taxonomic questions and identify new species. Neotropical fishes are found in a wide variety of shapes and sizes, with a large number of species yet to be described, many of which are very difficult to identify. Characidae is the most species-rich family of the Characiformes, and many of its genera are affected by taxonomic uncertainties, including the widely-distributed, species-rich genus Astyanax. In this study, we present an extensive analysis of Astyanax covering almost its entire area of occurrence, based on DNA barcoding. The use of different approaches (ABGD, GMYC and BIN) to the clustering of the sequences revealed ample consistency in the results obtained by the initial cutoff value of 2% divergence for putative species in the Neighbor-Joining analysis using the Kimura-2-parameter model. The results indicate the existence of five Astyanax lineages. Some groups, such as that composed by the trans-Andean forms, are mostly composed of well-defined species, and in others a number of nominal species are clustered together, hampering the delimitation of species, which in many cases proved impossible. The results confirm the extreme complexity of the systematics of the genus Astyanax and show that DNA barcoding can be an useful tool to address these complexes questions.
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Affiliation(s)
- Bruno César Rossini
- Laboratório de Biologia e Genética de Peixes, Departamento de Morfologia, UNESP—Universidade Estadual Paulista, Botucatu, São Paulo, Brazil
- Instituto de Biotecnologia da UNESP, UNESP—Universidade Estadual Paulista, Botucatu, São Paulo, Brazil
- * E-mail:
| | - Carlos Alexandre Miranda Oliveira
- Universidade Estadual de Maringá, Programa de Pós-Graduação em Ecologia de Ambientes Aquáticos Continentais, Maringá, Paraná, Brazil
| | | | - Vinicius de Araújo Bertaco
- Museu de Ciências Naturais, Fundação Zoobotânica do Rio Grande do Sul, Porto Alegre, Rio Grande do Sul, Brazil
| | - Juan M. Díaz de Astarloa
- Grupo de Biotaxonomía Morfológica y Molecular de Peces, Instituto de Investigaciones Marinas y Costeras, Universidad Nacional de Mar del Plata. Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
| | - Juan J. Rosso
- Grupo de Biotaxonomía Morfológica y Molecular de Peces, Instituto de Investigaciones Marinas y Costeras, Universidad Nacional de Mar del Plata. Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
| | - Fausto Foresti
- Laboratório de Biologia e Genética de Peixes, Departamento de Morfologia, UNESP—Universidade Estadual Paulista, Botucatu, São Paulo, Brazil
| | - Claudio Oliveira
- Laboratório de Biologia e Genética de Peixes, Departamento de Morfologia, UNESP—Universidade Estadual Paulista, Botucatu, São Paulo, Brazil
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Morphological and genetic divergence of a small stream fish species along a watershed. BIOCHEM SYST ECOL 2016. [DOI: 10.1016/j.bse.2016.06.007] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Laopichienpong N, Muangmai N, Supikamolseni A, Twilprawat P, Chanhome L, Suntrarachun S, Peyachoknagul S, Srikulnath K. Assessment of snake DNA barcodes based on mitochondrial COI and Cytb genes revealed multiple putative cryptic species in Thailand. Gene 2016; 594:238-247. [PMID: 27632899 DOI: 10.1016/j.gene.2016.09.017] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2015] [Revised: 08/24/2016] [Accepted: 09/11/2016] [Indexed: 12/21/2022]
Abstract
DNA barcodes of mitochondrial cytochrome c oxidase I (COI), cytochrome b (Cytb) genes, and their combined data sets were constructed from 35 snake species in Thailand. No barcoding gap was detected in either of the two genes from the observed intra- and interspecific sequence divergences. Intra- and interspecific sequence divergences of the COI gene differed 14 times, with barcode cut-off scores ranging over 2%-4% for threshold values differentiated among most of the different species; the Cytb gene differed 6 times with cut-off scores ranging over 2%-6%. Thirty-five specific nucleotide mutations were also found at interspecific level in the COI gene, identifying 18 snake species, but no specific nucleotide mutation was observed for Cytb in any single species. This suggests that COI barcoding was a better marker than Cytb. Phylogenetic clustering analysis indicated that most species were represented by monophyletic clusters, suggesting that these snake species could be clearly differentiated using COI barcodes. However, the two-marker combination of both COI and Cytb was more effective, differentiating snake species by over 2%-4%, and reducing species numbers in the overlap value between intra- and interspecific divergences. Three species delimitation algorithms (general mixed Yule-coalescent, automatic barcoding gap detection, and statistical parsimony network analysis) were extensively applied to a wide range of snakes based on both barcodes. This revealed cryptic diversity for eleven snake species in Thailand. In addition, eleven accessions from the database previously grouped under the same species were represented at different species level, suggesting either high genetic diversity, or the misidentification of these sequences in the database as a consequence of cryptic species.
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Affiliation(s)
- Nararat Laopichienpong
- Laboratory of Animal Cytogenetics and Comparative Genomics, Department of Genetics, Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand
| | - Narongrit Muangmai
- Department of Fishery Biology, Faculty of Fisheries, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand
| | - Arrjaree Supikamolseni
- Laboratory of Animal Cytogenetics and Comparative Genomics, Department of Genetics, Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand
| | - Panupon Twilprawat
- Laboratory of Animal Cytogenetics and Comparative Genomics, Department of Genetics, Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand
| | - Lawan Chanhome
- Snake Farm, Queen Saovabha Memorial Institute, The Thai Red Cross Society, Bangkok 10330, Thailand
| | - Sunutcha Suntrarachun
- Department of Research and Development, Queen Saovabha Memorial Institute, The Thai Red Cross Society, Bangkok 10330, Thailand
| | - Surin Peyachoknagul
- Laboratory of Animal Cytogenetics and Comparative Genomics, Department of Genetics, Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand; Center for Advanced Studies in Tropical Natural Resources, National Research University-Kasetsart University, Kasetsart University, Thailand (CASTNAR, NRU-KU), Thailand
| | - Kornsorn Srikulnath
- Laboratory of Animal Cytogenetics and Comparative Genomics, Department of Genetics, Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand; Center for Advanced Studies in Tropical Natural Resources, National Research University-Kasetsart University, Kasetsart University, Thailand (CASTNAR, NRU-KU), Thailand.
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Shen Y, Guan L, Wang D, Gan X. DNA barcoding and evaluation of genetic diversity in Cyprinidae fish in the midstream of the Yangtze River. Ecol Evol 2016; 6:2702-13. [PMID: 27066250 PMCID: PMC4798831 DOI: 10.1002/ece3.2060] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2015] [Revised: 01/31/2016] [Accepted: 02/02/2016] [Indexed: 11/29/2022] Open
Abstract
The Yangtze River is the longest river in China and is divided into upstream and mid-downstream regions by the Three Gorges (the natural barriers of the Yangtze River), resulting in a complex distribution of fish. Dramatic changes to habitat environments may ultimately threaten fish survival; thus, it is necessary to evaluate the genetic diversity and propose protective measures. Species identification is the most significant task in many fields of biological research and in conservation efforts. DNA barcoding, which constitutes the analysis of a short fragment of the mitochondrial cytochrome c oxidase subunit I (COI) sequence, has been widely used for species identification. In this study, we collected 561 COI barcode sequences from 35 fish from the midstream of the Yangtze River. The intraspecific distances of all species were below 2% (with the exception of Acheilognathus macropterus and Hemibarbus maculatus). Nevertheless, all species could be unambiguously identified from the trees, barcoding gaps and taxonomic resolution ratio values. Furthermore, the COI barcode diversity was found to be low (≤0.5%), with the exception of H. maculatus (0.87%), A. macropterus (2.02%) and Saurogobio dabryi (0.82%). No or few shared haplotypes were detected between the upstream and downstream populations for ten species with overall nucleotide diversities greater than 0.00%, which indicated the likelihood of significant population genetic structuring. Our analyses indicated that DNA barcoding is an effective tool for the identification of cyprinidae fish in the midstream of the Yangtze River. It is vital that some protective measures be taken immediately because of the low COI barcode diversity.
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Affiliation(s)
- Yanjun Shen
- The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of SciencesInstitute of HydrobiologyChinese Academy of SciencesWuhan430072HubeiChina
- University of Chinese Academy of SciencesBeijing100039China
| | - Lihong Guan
- College of Life Science and TechnologyXinxiang Medical UniversityHe'nan Xinxiang453003China
| | - Dengqiang Wang
- The Key Laboratory of Freshwater Biodiversity ConservationMinistry of AgricultureYangtze River Fisheries Research InstituteChinese Academy of Fishery SciencesWuhanChina
| | - Xiaoni Gan
- The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of SciencesInstitute of HydrobiologyChinese Academy of SciencesWuhan430072HubeiChina
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Cardoso AL, Carvalho HLS, Benathar TCM, Serrão SMG, Nagamachi CY, Pieczarka JC, Sousa LMD, Ready JS, Noronha RCR. Integrated Cytogenetic and Mitochondrial DNA Analyses Indicate That Two Different Phenotypes of Hypancistrus (L066 and L333) Belong to the Same Species. Zebrafish 2016; 13:209-16. [PMID: 26983010 DOI: 10.1089/zeb.2015.1213] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The diversity of Hypancistrus species in the Xingu River is remarkable and the variation in color morphs represents a real challenge to taxonomists to delimit species boundaries. One of the most recognizable Hypancistrus complexes is the worm-lined species, known in the aquarium trade as King Tiger Plec in English, Hypancistrus "pão" in Portuguese or under the L-numbers L066 and L333 that represent two melanic pigment pattern phenotypes. To assess the identity of these two phenotypes, we described their karyotypes and sequenced part of the mitochondrial cytochrome oxidase I gene (DNA barcode). These fishes have 52 chromosomes (40 meta-submetacentric and 12 subtelo-acrocentric) and a strong heteromorphism in chromosome pair 21 was observed, which does not correlate with the two phenotypes or sex. DNA barcodes separated the samples analyzed from Hypancistrus zebra and other publicly available sequences of Loricariidae showing no divergence between the two phenotypes. The data set indicates that worm-lined Hypancistrus from the Xingu form a single species with clear chromosomal and melanic pigment pattern polymorphisms.
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Affiliation(s)
- Adauto Lima Cardoso
- 1 Laboratório de Citogenética, Centro de Estudos Avançados da Biodiversidade, Instituto de Ciências Biológicas, Universidade Federal do Pará , Belém, Pará, Brazil
| | - Hagi Lopescu Silva Carvalho
- 1 Laboratório de Citogenética, Centro de Estudos Avançados da Biodiversidade, Instituto de Ciências Biológicas, Universidade Federal do Pará , Belém, Pará, Brazil
| | - Thayse Cristine Melo Benathar
- 1 Laboratório de Citogenética, Centro de Estudos Avançados da Biodiversidade, Instituto de Ciências Biológicas, Universidade Federal do Pará , Belém, Pará, Brazil
| | - Suellen Maria Gales Serrão
- 2 Laboratório de Lepidopterologia e Ictiologia Integrada, Centro de Estudos Avançados da Biodiversidade, Instituto de Ciências Biológicas, Universidade Federal do Pará , Belém, Pará, Brazil
| | - Cleusa Yoshiko Nagamachi
- 1 Laboratório de Citogenética, Centro de Estudos Avançados da Biodiversidade, Instituto de Ciências Biológicas, Universidade Federal do Pará , Belém, Pará, Brazil
| | - Julio Cesar Pieczarka
- 1 Laboratório de Citogenética, Centro de Estudos Avançados da Biodiversidade, Instituto de Ciências Biológicas, Universidade Federal do Pará , Belém, Pará, Brazil
| | - Leandro Melo de Sousa
- 3 Faculdade de Ciências Biológicas, Universidade Federal do Pará , Campus de Altamira, Altamira, Pará, Brazil
| | - Jonathan Stuart Ready
- 2 Laboratório de Lepidopterologia e Ictiologia Integrada, Centro de Estudos Avançados da Biodiversidade, Instituto de Ciências Biológicas, Universidade Federal do Pará , Belém, Pará, Brazil
| | - Renata Coelho Rodrigues Noronha
- 1 Laboratório de Citogenética, Centro de Estudos Avançados da Biodiversidade, Instituto de Ciências Biológicas, Universidade Federal do Pará , Belém, Pará, Brazil
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Ordoñez JFF, Ventolero MFH, Santos MD. Maternal mismatches in farmed tilapia strains (Oreochromis spp.) in the Philippines as revealed by mitochondrial COI gene. Mitochondrial DNA A DNA Mapp Seq Anal 2016; 28:526-535. [PMID: 27159705 DOI: 10.3109/24701394.2016.1149824] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
The introduction of genetically enhanced tilapia has significantly boosted the performance of Philippine aquaculture industry. While enhanced strains contribute to the increase in tilapia production, genetic characterization of present tilapia stocks is critical to maintain their quality and to ensure the genetic gains are sustained. To understand and determine the genetic relationship of the genetically enhanced strains produced in the Philippines, mitochondrial cytochrome oxidase subunit I (COI) gene using DNA barcoding approach was analyzed. Specimens representing 10 genetically enhanced strains (GIFT, FaST, GET-EXCEL, GST, SST, COLD, YY-male, GMT, Molobicus, and BEST), three red tilapia (Taiwan red, Florida red, and FAC-red), and two pure lines (initially identified as O. aureus and O. spilurus) were collected, sequenced, and identified using DNA barcoding. Results revealed that farmed tilapias consisted of four different Oreochromis species. As expected, COI could not distinguish individuals at the strain level but surprisingly, mismatch between the species of maternal origin and present-day offspring was observed. This particular result may pose a question on the genetic purity and integrity of the strains being distributed to farmers and suggests a re-evaluation of the effectiveness of major tilapia breeding centers in maintaining their stocks.
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Affiliation(s)
- June Feliciano F Ordoñez
- a Genetic Fingerprinting Laboratory - National Fisheries Research and Development Institute , Quezon City , South Triangle , Philippines
| | - Minerva Fatimae H Ventolero
- a Genetic Fingerprinting Laboratory - National Fisheries Research and Development Institute , Quezon City , South Triangle , Philippines
| | - Mudjekeewis D Santos
- a Genetic Fingerprinting Laboratory - National Fisheries Research and Development Institute , Quezon City , South Triangle , Philippines
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Melo BF, Ochoa LE, Vari RP, Oliveira C. Cryptic species in the Neotropical fish genusCurimatopsis(Teleostei, Characiformes). ZOOL SCR 2016. [DOI: 10.1111/zsc.12178] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Affiliation(s)
- Bruno F. Melo
- Departamento de Morfologia, Instituto de Biociências; Universidade Estadual Paulista; Distr. Rubião Jr. s/n 18618-970 Botucatu São Paulo Brazil
- Department of Vertebrate Zoology; National Museum of Natural History, Smithsonian Institution; 20013-7012 Washington DC USA
| | - Luz E. Ochoa
- Departamento de Morfologia, Instituto de Biociências; Universidade Estadual Paulista; Distr. Rubião Jr. s/n 18618-970 Botucatu São Paulo Brazil
| | - Richard P. Vari
- Department of Vertebrate Zoology, MCR-159; National Museum of Natural History, Smithsonian Institution; PO Box 37012 20013-7012 Washington DC USA
| | - Claudio Oliveira
- Departamento de Morfologia, Instituto de Biociências; Universidade Estadual Paulista; Distr. Rubião Jr. s/n 18618-970 Botucatu São Paulo Brazil
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Jose D, Harikrishnan M. Non-homologous COI barcode regions: a serious concern in decapod molecular taxonomy. Mitochondrial DNA A DNA Mapp Seq Anal 2016; 28:482-492. [DOI: 10.3109/19401736.2015.1137902] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Affiliation(s)
- Deepak Jose
- School of Industrial Fisheries, Cochin University of Science and Technology, Kochi, Kerala, India
| | - Mahadev Harikrishnan
- School of Industrial Fisheries, Cochin University of Science and Technology, Kochi, Kerala, India
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Muhammad Tahir H, Akhtar S. Services of DNA barcoding in different fields. Mitochondrial DNA A DNA Mapp Seq Anal 2015; 27:4463-4474. [DOI: 10.3109/19401736.2015.1089572] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
| | - Samreen Akhtar
- Department of Zoology, University of Sargodha, Sargodha, Pakistan
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Using Different Methods to Access the Difficult Task of Delimiting Species in a Complex Neotropical Hyperdiverse Group. PLoS One 2015; 10:e0135075. [PMID: 26332320 PMCID: PMC4557985 DOI: 10.1371/journal.pone.0135075] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2015] [Accepted: 07/16/2015] [Indexed: 11/19/2022] Open
Abstract
The genus Rineloricaria is a Neotropical freshwater fish group with a long and problematic taxonomic history, attributed to the large number of species and the pronounced similarity among them. In the present work, taxonomic information and different molecular approaches were used to identify species boundaries and characterize independent evolutionary units. We analyzed 228 samples assembled in 53 distinct morphospecies. A general mixed yule-coalescent (GMYC) analysis indicated the existence of 70 entities, while BOLD system analyses showed the existence of 56 distinct BINs. When we used a new proposed integrative taxonomy approach, mixing the results obtained by each analysis, we identified 73 OTUs. We suggest that Rineloricaria probably has some complexity in the known species and several species not formally described yet. Our data suggested that other hyperdiverse fish groups with wide distributions can be further split into many new evolutionary taxonomic units.
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42
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Escobar-Camacho D, Barriga R, Ron SR. Discovering Hidden Diversity of Characins (Teleostei: Characiformes) in Ecuador's Yasuní National Park. PLoS One 2015; 10:e0135569. [PMID: 26275041 PMCID: PMC4537159 DOI: 10.1371/journal.pone.0135569] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2014] [Accepted: 07/23/2015] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND Management and conservation of biodiversity requires adequate species inventories. The Yasuní National Park is one of the most diverse regions on Earth and recent studies of terrestrial vertebrates, based on genetic evidence, have shown high levels of cryptic and undescribed diversity. Few genetic studies have been carried out in freshwater fishes from western Amazonia. Thus, in contrast with terrestrial vertebrates, their content of cryptic diversity remains unknown. In this study, we carried out genetic and morphological analyses on characin fishes at Yasuní National Park, in eastern Ecuador. Our goal was to identify cryptic diversity among one of the most speciose fish families in the Amazon region. This is the first time that genetic evidence has been used to assess the species content of the Napo Basin, one of the richest regions in vertebrate diversity. RESULTS Phylogenetic analyses of partial mitochondrial 16S ribosomal RNA gene (∼600 pb) DNA sequences from 232 specimens of the family Characidae and its closest groups revealed eight candidate new species among 33 species sampled, representing a 24% increase in species number. Analyses of external morphology allowed us to confirm the species status of six of the candidate species. CONCLUSIONS Our results show high levels of cryptic diversity in Amazonian characins. If this group is representative of other Amazonian fish, our results would imply that the species richness of the Amazonian ichthyofauna is highly underestimated. Molecular methods are a necessary tool to obtain more realistic inventories of Neotropical freshwater fishes.
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Affiliation(s)
- Daniel Escobar-Camacho
- Museo de Zoología, Escuela de Biología, Pontificia Universidad Católica del Ecuador, Quito, Pichincha, Ecuador
- Museo de Ictiología, Museo de Historia Natural Gustavo Orces, Instituto de Ciencias Biológicas, Escuela Politécnica Nacional, Quito, Pichincha, Ecuador
| | - Ramiro Barriga
- Museo de Ictiología, Museo de Historia Natural Gustavo Orces, Instituto de Ciencias Biológicas, Escuela Politécnica Nacional, Quito, Pichincha, Ecuador
| | - Santiago R. Ron
- Museo de Zoología, Escuela de Biología, Pontificia Universidad Católica del Ecuador, Quito, Pichincha, Ecuador
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Jose D, Nidhin B, Anil Kumar KP, Pradeep PJ, Harikrishnan M. A molecular approach towards the taxonomy of fresh water prawns Macrobrachium striatum and M. equidens (Decapoda, Palaemonidae) using mitochondrial markers. Mitochondrial DNA A DNA Mapp Seq Anal 2015; 27:2585-93. [PMID: 26119113 DOI: 10.3109/19401736.2015.1041114] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Genus Macrobrachium includes freshwater prawns which inhabit most diverse habitats ranging from low saline areas to inland hill streams and impounded water bodies. Being morphologically conserved, this genus has been exposed to severe disputes related to their taxonomy, systematics and phylogeny. Macrobrachium striatum and M. equidens represent two morphologically related congeneric species within this genus. Earlier, M. striatum was considered as a striped form of M. equidens. Though these species are now well-described morphologically and differentiated into two species, no molecular level investigation has been carried out in support of their speciation. We report a study on M. striatum and M. equidens with emphasis to their molecular data through mitochondrial markers (16S ribosomal RNA and cytochrome oxidase subunit I). Results obtained from developed molecular markers of the two species revealed considerable genetic differentiation between them. Phylogram generated using Minimum evolution and Neighbour joining analyses differentiated M. striatum and M. equidens as two independent species. Genetic distance data showed high interspecific divergence (ranging from 3.9% to 17.0% for 16S rRNA sequences and 13.8% to 21.0% for COI sequences) between M. striatum and M. equidens confirming the findings of phylogram. Hence, it could be delineated that M. striatum and M. equidens represent two distinct species within genus Macrobrachium with emphasis to their morphology and genetics.
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Affiliation(s)
- Deepak Jose
- a CUSAT, School of Industrial Fisheries , Fine Arts Avenue , Kochi , Kerala , India and
| | - B Nidhin
- a CUSAT, School of Industrial Fisheries , Fine Arts Avenue , Kochi , Kerala , India and
| | - K P Anil Kumar
- a CUSAT, School of Industrial Fisheries , Fine Arts Avenue , Kochi , Kerala , India and
| | - P J Pradeep
- b Department of Anatomy and Centex Shrimp, Faculty of Science , Mahidol University , Bangkok , Thailand
| | - M Harikrishnan
- a CUSAT, School of Industrial Fisheries , Fine Arts Avenue , Kochi , Kerala , India and
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44
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Ochoa LE, Pereira LHG, Costa-Silva GJ, Roxo FF, Batista JS, Formiga K, Foresti F, Oliveira C. Genetic structure and historical diversification of catfish Brachyplatystoma platynemum (Siluriformes: Pimelodidae) in the Amazon basin with implications for its conservation. Ecol Evol 2015; 5:2005-20. [PMID: 26045952 PMCID: PMC4449755 DOI: 10.1002/ece3.1486] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2014] [Revised: 03/11/2015] [Accepted: 03/23/2015] [Indexed: 11/16/2022] Open
Abstract
Brachyplatystoma platynemum is a catfish species widely distributed in the Amazon basin. Despite being considered of little commercial interest, the decline in other fish populations has contributed to the increase in the catches of this species. The structure, population genetic variability, and evolutionary process that have driven the diversification of this species are presently unknown. Considering that, in order to better understand the genetic structure of this species, we analyzed individuals from seven locations of the Amazon basin using eight molecular markers: control region and cytochrome b mtDNA sequences, and a set of six nuclear microsatellite loci. The results show high levels of haplotype diversity and point to the occurrence of two structured populations (Amazon River and the Madeira River) with high values for F ST. Divergence time estimates based on mtDNA indicated that these populations diverged about 1.0 Mya (0.2-2.5 Mya 95% HPD) using cytochrome b and 1.4 Mya (0.2-2.7 Mya 95% HPD) using control region. During that time, the influence of climate changes and hydrological events such as sea level oscillations and drainage isolation as a result of geological processes in the Pleistocene may have contributed to the current structure of B. platynemum populations, as well as of differences in water chemistry in Madeira River. The strong genetic structure and the time of genetic divergence estimated for the groups may indicate the existence of strong structure populations of B. platynemum in the Amazon basin.
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Affiliation(s)
- Luz Eneida Ochoa
- Departamento de Morfologia, Instituto de Biociências de Botucatu, Universidade Estadual PaulistaSão Paulo, Brazil
| | - Luiz Henrique G Pereira
- Centro Interdisciplinar de Ciências da Vida, Universidade Federal da Integração Latino AmericanaFoz do Iguaçu, Brazil
| | - Guilherme Jose Costa-Silva
- Departamento de Morfologia, Instituto de Biociências de Botucatu, Universidade Estadual PaulistaSão Paulo, Brazil
| | - Fábio F Roxo
- Departamento de Morfologia, Instituto de Biociências de Botucatu, Universidade Estadual PaulistaSão Paulo, Brazil
| | - Jacqueline S Batista
- Laboratório Temático de Biologia Molecular, Instituto Nacional de Pesquisa da AmazôniaManaus, Brazil
| | - Kyara Formiga
- Laboratório Temático de Biologia Molecular, Instituto Nacional de Pesquisa da AmazôniaManaus, Brazil
| | - Fausto Foresti
- Departamento de Morfologia, Instituto de Biociências de Botucatu, Universidade Estadual PaulistaSão Paulo, Brazil
| | - Claudio Oliveira
- Departamento de Morfologia, Instituto de Biociências de Botucatu, Universidade Estadual PaulistaSão Paulo, Brazil
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45
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de Brito MA, Schneider H, Sampaio I, Santos S. DNA barcoding reveals high substitution rate and mislabeling in croaker fillets (Sciaenidae) marketed in Brazil: The case of “pescada branca” (Cynoscion leiarchus and Plagioscion squamosissimus). Food Res Int 2015. [DOI: 10.1016/j.foodres.2015.01.031] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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46
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Frantine-Silva W, Sofia SH, Orsi ML, Almeida FS. DNA barcoding of freshwater ichthyoplankton in the Neotropics as a tool for ecological monitoring. Mol Ecol Resour 2015; 15:1226-37. [PMID: 25655460 DOI: 10.1111/1755-0998.12385] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2014] [Revised: 01/30/2015] [Accepted: 02/02/2015] [Indexed: 11/26/2022]
Abstract
Quantifying and classifying ichthyoplankton is one of the most effective ways of monitoring the recruitment process in fishes. However, correctly identifying the fish based on morphological characters is extremely difficult, especially in the early stages of development. We examined ichthyoplankton from tributaries and reservoirs along the middle stretch of the Paranapanema River, one of the areas most impacted by hydroelectric projects in the Neotropics. Matching DNA sequences of the COI gene (628-648 bp) allowed us to identify 99.25% of 536 samples of eggs (293) and larvae (243) subjected to BOLD-IDS similarity analysis with a species-level threshold of 1.3%. The results revealed 37 species in 27 genera, 15 families and four orders, some 23.8% of documented fish species in the Paranapanema River. Molecular identification meant that we could include data from egg samples that accounted for about 30% of the species richness observed. The results in this study confirm the efficacy of DNA barcoding in identifying Neotropical ichthyoplankton and show how the data produced provide valuable information for preparing plans for conserving and managing inland waters.
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Affiliation(s)
- W Frantine-Silva
- Departamento de Biologia Geral, Universidade Estadual de Londrina, Centro de Ciências Biológicas, Campus Universitário, Rodovia Celso Garcia Cid, PR 445 km 380, 86057-970, Londrina-PR, Brasil
| | - S H Sofia
- Departamento de Biologia Geral, Universidade Estadual de Londrina, Centro de Ciências Biológicas, Campus Universitário, Rodovia Celso Garcia Cid, PR 445 km 380, 86057-970, Londrina-PR, Brasil
| | - M L Orsi
- Departamento de Biologia Animal e Vegetal, Universidade Estadual de Londrina, Centro de Ciências Biológicas, Campus Universitário, Rodovia Celso Garcia Cid, PR 445 km 380, 86057-970, Londrina-PR, Brasil
| | - F S Almeida
- Departamento de Biologia Geral, Universidade Estadual de Londrina, Centro de Ciências Biológicas, Campus Universitário, Rodovia Celso Garcia Cid, PR 445 km 380, 86057-970, Londrina-PR, Brasil
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Loh WKW, Bond P, Ashton KJ, Roberts DT, Tibbetts IR. DNA barcoding of freshwater fishes and the development of a quantitative qPCR assay for the species-specific detection and quantification of fish larvae from plankton samples. JOURNAL OF FISH BIOLOGY 2014; 85:307-328. [PMID: 24963726 DOI: 10.1111/jfb.12422] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/11/2013] [Accepted: 04/11/2014] [Indexed: 06/03/2023]
Abstract
The barcoding of mitochondrial cytochrome c oxidase subunit 1 (coI) gene was amplified and sequenced from 16 species of freshwater fishes found in Lake Wivenhoe (south-eastern Queensland, Australia) to support monitoring of reservoir fish populations, ecosystem function and water health. In this study, 630-650 bp sequences of the coI barcoding gene from 100 specimens representing 15 genera, 13 families and two subclasses of fishes allowed 14 of the 16 species to be identified and differentiated. The mean ± s.e. Kimura 2 parameter divergence within and between species was 0.52 ± 0.10 and 23.8 ± 2.20% respectively, indicating that barcodes can be used to discriminate most of the fish species accurately. The two terapontids, Amniataba percoides and Leiopotherapon unicolor, however, shared coI DNA sequences and could not be differentiated using this gene. A barcoding database was established and a qPCR assay was developed using coI sequences to identify and quantify proportional abundances of fish species in ichthyoplankton samples from Lake Wivenhoe. These methods provide a viable alternative to the time-consuming process of manually enumerating and identifying ichthyoplankton samples.
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Affiliation(s)
- W K W Loh
- School of Biological Sciences, University of Queensland, St Lucia, Qld 4072, Australia
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48
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Chakraborty M, Ghosh SK. An assessment of the DNA barcodes of Indian freshwater fishes. Gene 2014; 537:20-8. [DOI: 10.1016/j.gene.2013.12.047] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2013] [Revised: 12/13/2013] [Accepted: 12/18/2013] [Indexed: 11/17/2022]
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49
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Ribeiro AC, Jacob RM, Silva RRSR, Lima FCT, Ferreira DC, Ferreira KM, Mariguela TC, Pereira LHG, Oliveira C. Distributions and phylogeographic data of rheophilic freshwater fishes provide evidences on the geographic extension of a central-brazilian amazonian palaeoplateau in the area of the present day Pantanal Wetland. NEOTROPICAL ICHTHYOLOGY 2013. [DOI: 10.1590/s1679-62252013000200010] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The analysis of the distribution patterns presented by examples of freshwater fishes restricted to headwater habitat: the anostomid Leporinus octomaculatus, the characins Jubiaba acanthogaster, Oligosarcus perdido, Moenkhausia cosmops, Knodus chapadae, Planaltina sp., the loricariid Hypostomus cochliodon, and the auchenipterid Centromochlus sp. provided evidences of a relatively recent shared history between the highlands of the upper rio Paraguay and adjoining upland drainage basins. Restricted to headwater of the uplands in the upper rio Paraguay and adjoining basins, these species provide biological evidence of the former extension of the central Brazilian plateau before the origin of the Pantanal Wetland. Disjunction took place due to an ecological barrier to these rheophilic taxa represented tectonic subsidence related to the origin of the Pantanal Wetland. Molecular analysis of Jubiaba acanthogaster revealed that the sample from the upper rio Xingu basin are the sister-group of a clade that includes samples from the upper rio Arinos (upper rio Tapajós) plus the upper rio Paraguay basin, supporting the assumption that the origin of the upper rio Paraguay basin causing vicariance between this basin and the upper rio Tapajós is the least vicariant event in the evolutionary history of the group.
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50
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Pereira LHG, Hanner R, Foresti F, Oliveira C. Can DNA barcoding accurately discriminate megadiverse Neotropical freshwater fish fauna? BMC Genet 2013; 14:20. [PMID: 23497346 PMCID: PMC3608943 DOI: 10.1186/1471-2156-14-20] [Citation(s) in RCA: 156] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2012] [Accepted: 03/05/2013] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The megadiverse Neotropical freshwater ichthyofauna is the richest in the world with approximately 6,000 recognized species. Interestingly, they are distributed among only 17 orders, and almost 80% of them belong to only three orders: Characiformes, Siluriformes and Perciformes. Moreover, evidence based on molecular data has shown that most of the diversification of the Neotropical ichthyofauna occurred recently. These characteristics make the taxonomy and identification of this fauna a great challenge, even when using molecular approaches. In this context, the present study aimed to test the effectiveness of the barcoding methodology (COI gene) to identify the mega diverse freshwater fish fauna from the Neotropical region. For this purpose, 254 species of fishes were analyzed from the Upper Parana River basin, an area representative of the larger Neotropical region. RESULTS Of the 254 species analyzed, 252 were correctly identified by their barcode sequences (99.2%). The main K2P intra- and inter-specific genetic divergence values (0.3% and 6.8%, respectively) were relatively low compared with similar values reported in the literature, reflecting the higher number of closely related species belonging to a few higher taxa and their recent radiation. Moreover, for 84 pairs of species that showed low levels of genetic divergence (<2%), application of a complementary character-based nucleotide diagnostic approach proved useful in discriminating them. Additionally, 14 species displayed high intra-specific genetic divergence (>2%), pointing to at least 23 strong candidates for new species. CONCLUSIONS Our study is the first to examine a large number of freshwater fish species from the Neotropical area, including a large number of closely related species. The results confirmed the efficacy of the barcoding methodology to identify a recently radiated, megadiverse fauna, discriminating 99.2% of the analyzed species. The power of the barcode sequences to identify species, even with low interspecific divergence, gives us an idea of the distribution of inter-specific genetic divergence in these megadiverse fauna. The results also revealed hidden genetic divergences suggestive of reproductive isolation and putative cryptic speciation in some species (23 candidates for new species). Finally, our study constituted an important contribution to the international Barcoding of Life (iBOL.org) project, providing barcode sequences for use in identification of these species by experts and non-experts, and allowing them to be available for use in other applications.
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Affiliation(s)
- Luiz H G Pereira
- Laboratory of Biology and Genetic of Fish, Department of Morphology, Biosciences Institute, State University of São Paulo, São Paulo, Brazil.
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