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de Oliveira Dias J, Zanchi FB, Zacardi DM, Oliveira LS, de Vargas Schons S, Sousa RGC. Population structure and reproductive indicators of the surubim Pseudoplatystoma punctifer (Siluriformes, Pimelodidae) in the São Miguel River, Amazon basin, Brazil. JOURNAL OF FISH BIOLOGY 2024; 104:1764-1774. [PMID: 38450744 DOI: 10.1111/jfb.15714] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Revised: 01/22/2024] [Accepted: 02/19/2024] [Indexed: 03/08/2024]
Abstract
Fish is an important source of food and income for a significant portion of the Amazonian population, especially those who live along the rivers and lakes in the region. Pseudoplatystoma punctifer (Castelnau, 1855), known as surubim, is a species of Neotropical catfish widely exploited by fisheries and commercially valuable in the Guaporé River basin, Brazil. However, population dynamics are poorly known in the region. To understand the population structure and reproductive biology aspects of the surubim, monthly experimental fisheries were carried out in the São Miguel River, state of Rondônia, Brazil, between August 2020 and July 2021. The captured fish were weighed, and its gonads were removed and weighed for histological analyses (microscopic description) and classification of the maturation stages (macroscopic description). The collected gonads were fixed in 10% buffered formalin, dehydrated, cut into 4-μm-thick sections, and stained with hematoxylin and eosin. A total of 34 individuals were collected (20 females and 14 males), showing positive allometric growth and condition factor from 0.81 to 1.79 for females and males, respectively. Females were larger in size and weight than males. P. punctifer reaches its first maturation at an average length of 68.30 cm, indicating the importance of respecting the minimum capture size as an alternative to ensure the natural stocks of this fishery resource in the region. The results provide support for the establishment of public policies and actions for conservation, management, and regulation of fishing.
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Affiliation(s)
- Jordy de Oliveira Dias
- Departamento de Zootecnia, Universidade Federal de Rondônia (UNIR), Presidente Médici, Brazil
| | - Fabrício Berton Zanchi
- Núcleo de Pesquisas em Ecossistemas Tropicais do Centro de Formação em Ciências Ambientais, CFCAm da Universidade Federal do Sul da Bahia (UFSB), Porto Seguro, Brazil
| | - Diego Maia Zacardi
- Universidade Federal do Oeste do Pará (UFOPA), Laboratório de Ecologia do Ictioplâncton e Pesca em Águas Interiores, Instituto de Ciências e Tecnologia das Águas, Santarém, Brazil
- Programa de Pós-graduação em Biodiversidade, Universidade Federal do Oeste do Pará (UFOPA), Santarém, Brazil
| | - Lucas Silva Oliveira
- Universidade Federal do Oeste do Pará (UFOPA), Laboratório de Ecologia do Ictioplâncton e Pesca em Águas Interiores, Instituto de Ciências e Tecnologia das Águas, Santarém, Brazil
- Programa de Pós-graduação em Ecologia, Universidade Federal do Pará (UFPA), Belém, Brazil
| | - Sandro de Vargas Schons
- Programa de Pós-graduação em Ciências Ambientais, Universidade Federal de Rondônia (UNIR), Rolim de Moura, Brazil
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Lira NL, Tonello S, Lui RL, Traldi JB, Brandão H, Oliveira C, Blanco DR. Identifying fish eggs and larvae: from classic methodologies to DNA metabarcoding. Mol Biol Rep 2023; 50:1713-1726. [PMID: 36418775 DOI: 10.1007/s11033-022-08091-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Accepted: 11/04/2022] [Indexed: 11/25/2022]
Abstract
Studies involving fish eggs and larvae date back to the end of the nineteenth century. Since then, studies with ichthyoplankton have proved to be an essential tool, generating information for the knowledge of the ichthyofauna and the environmental inventory. Most of these studies reveal the difficulty of obtaining a precise taxonomic identification of the collected materials, making research with ichthyoplankton extremely challenging. With the advent of molecular biology, the use of markers such as COI enabled greater taxonomic precision, helping to understand events involving ichthyofauna. Now we can observe the evolution of the molecular identification tool for ichthyoplankton via DNA barcoding, which has been increasingly used over the last few decades. From 2000 to 2010, we found six publications; from 2011 to 2021, 75 papers were published, and in 2022 four studies. Our survey also showed the accuracy of molecular identification when compared to the taxonomic identification of these. In this review, we show the state of the art of studies that used barcode and DNA metabarcoding to identify fish eggs and larvae in different environments and discuss their importance as the best practice for working with these organisms.
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Affiliation(s)
- Natália Lima Lira
- Programa de Pós-Graduação em Recursos Naturais e Sustentabilidade, Universidade Tecnológica Federal do Paraná, Prolongamento da Rua Cerejeira, S/N, Santa Helena, PR, 85892-000, Brazil.
| | - Sandro Tonello
- Programa de Pós-Graduação em Genética, Conservação e Biologia Evolutiva, Instituto Nacional de Pesquisas da Amazônia, Av. André Araújo, 2936, Aleixo, Manaus, AM, 69080-971, Brazil
| | - Roberto Laridondo Lui
- Centro de Ciências Biológicas e da Saúde, Universidade Estadual do Oeste do Paraná, R. Universitária, 1619, Cascavel, PR, 85819-170, Brazil
| | - Josiane Baccarin Traldi
- Instituto de Ciências Biológicas, Departamento de Genética, Universidade Federal do Amazonas, Av. General Rodrigo Octavio, 6200, Manaus, AM, 69080-900, Brazil
| | - Heleno Brandão
- Programa de Pós-Graduação em Recursos Naturais e Sustentabilidade, Universidade Tecnológica Federal do Paraná, Prolongamento da Rua Cerejeira, S/N, Santa Helena, PR, 85892-000, Brazil
| | - Claudio Oliveira
- Departamento de Biologia Estrutural e Funcional, Instituto de Biociências, Universidade Estadual Paulista, R. Prof. Dr. Antônio C. W. Zanin, 250, Botucatu, SP, 18618-689, Brazil
| | - Daniel Rodrigues Blanco
- Programa de Pós-Graduação em Recursos Naturais e Sustentabilidade, Universidade Tecnológica Federal do Paraná, Prolongamento da Rua Cerejeira, S/N, Santa Helena, PR, 85892-000, Brazil
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Breitbart M, Kerr M, Schram MJ, Williams I, Koziol G, Peebles E, Stallings CD. Evaluation of DNA metabarcoding for identifying fish eggs: a case study on the West Florida Shelf. PeerJ 2023; 11:e15016. [PMID: 36935909 PMCID: PMC10019330 DOI: 10.7717/peerj.15016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Accepted: 02/17/2023] [Indexed: 03/14/2023] Open
Abstract
A critical factor in fisheries management is the protection of spawning sites for ecologically and economically important fish species. DNA barcoding (i.e., amplification and sequencing of the mitochondrial cytochrome c oxidase I (COI) gene) of fish eggs has emerged as a powerful technique for identifying spawning sites. However, DNA barcoding of individual fish eggs is time-consuming and expensive. In an attempt to reduce costs and effort for long-term fisheries monitoring programs, here we used DNA metabarcoding, in which DNA is extracted and amplified from a composited sample containing all the fish eggs collected at a given site, to identify fish eggs from 49 stations on the West Florida Shelf. A total of 37 taxa were recovered from 4,719 fish eggs. Egg distributions on the West Florida Shelf corresponded with the known habitat types occupied by these taxa, which included burrower, coastal pelagic, epipelagic, mesopelagic, demersal, deep demersal, commensal, and reef-associated taxa. Metabarcoding of fish eggs was faster and far less expensive than barcoding individual eggs; however, this method cannot provide absolute taxon proportions due to variable copy numbers of mitochondrial DNA in different taxa, different numbers of cells within eggs depending on developmental stage, and PCR amplification biases. In addition, some samples yielded sequences from more taxa than the number of eggs present, demonstrating the presence of contaminating DNA and requiring the application of a threshold proportion of sequences required for counting a taxon as present. Finally, we review the advantages and disadvantages of using metabarcoding vs. individual fish egg barcoding for long-term monitoring programs.
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Mariac C, Duponchelle F, Miranda G, Ramallo C, Wallace R, Tarifa G, Garcia-Davila C, Ortega H, Pinto J, Renno JF. Unveiling biogeographical patterns of the ichthyofauna in the Tuichi basin, a biodiversity hotspot in the Bolivian Amazon, using environmental DNA. PLoS One 2022; 17:e0262357. [PMID: 34982802 PMCID: PMC8726463 DOI: 10.1371/journal.pone.0262357] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Accepted: 12/21/2021] [Indexed: 11/18/2022] Open
Abstract
To date, more than 2400 valid fish species have been recorded in the Amazon basin. However, some regions remain poorly documented. This is the case in the Beni basin and in particular in one of its main sub-basins, the Tuichi, an Andean foothills rivers flowing through the Madidi National Park in the Bolivian Amazonia. The knowledge of its ichthyological diversity is, however, essential for the management and protection of aquatic ecosystems, which are threatened by the development of infrastructures (dams, factories and cities), mining and deforestation. Environmental DNA (eDNA) has been relatively little used so far in the Amazon basin. We sampled eDNA from water in 34 sites in lakes and rivers in the Beni basin including 22 sites in the Tuichi sub-basin, during the dry season. To assess the biogeographical patterns of the amazonian ichthyofauna, we implemented a metabarcoding approach using two pairs of specific primers designed and developed in our laboratory to amplify two partially overlapping CO1 fragments, one of 185bp and another of 285bp. We detected 252 fish taxa (207 at species level) among which 57 are newly identified for the Beni watershed. Species compositions are significantly different between lakes and rivers but also between rivers according to their hydrographic rank and altitude. Furthermore, the diversity patterns are related to the different hydro-ecoregions through which the Tuichi flows. The eDNA approach makes it possible to identify and complete the inventory of the ichthyofauna in this still poorly documented Amazon basin. However, taxonomic identification remains constrained by the lack of reference barcodes in public databases and does not allow the assignment of all OTUs. Our results can be taken into account in conservation and management strategies and could serve as a baseline for future studies, including on other Andean tributaries.
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Affiliation(s)
- Cédric Mariac
- DIADE, Univ Montpellier, CIRAD, IRD, Montpellier, France
- Laboratoire Mixte International—Evolution et Domestication de l’Ichtyofaune Amazonienne (LMI—EDIA), IIAP, UAGRM, IRD, Paris, France
- * E-mail:
| | - Fabrice Duponchelle
- Laboratoire Mixte International—Evolution et Domestication de l’Ichtyofaune Amazonienne (LMI—EDIA), IIAP, UAGRM, IRD, Paris, France
- MARBEC, Univ Montpellier, CNRS, Ifremer, IRD, Montpellier, France
| | - Guido Miranda
- Laboratoire Mixte International—Evolution et Domestication de l’Ichtyofaune Amazonienne (LMI—EDIA), IIAP, UAGRM, IRD, Paris, France
- Wildlife Conservation Society, Bolivia Program, La Paz, Bolivia
- Unidad de Limnología, Instituto de Ecología, Universidad Mayor de San Andrés, La Paz, Bolivia
| | - Camila Ramallo
- Wildlife Conservation Society, Bolivia Program, La Paz, Bolivia
| | - Robert Wallace
- Wildlife Conservation Society, Bolivia Program, La Paz, Bolivia
| | - Gabriel Tarifa
- Wildlife Conservation Society, Bolivia Program, La Paz, Bolivia
| | - Carmen Garcia-Davila
- Laboratoire Mixte International—Evolution et Domestication de l’Ichtyofaune Amazonienne (LMI—EDIA), IIAP, UAGRM, IRD, Paris, France
- Instituto de Investigaciones de la Amazonía Peruana (IIAP), Laboratorio de Biología y Genética Molecular (LBGM), Iquitos, Perú
| | - Hernán Ortega
- Departamento de Ictiología, Museo de Historia Natural, Universidad Nacional Mayor San Marcos, Lima, Peru
| | - Julio Pinto
- Unidad de Limnología, Instituto de Ecología, Universidad Mayor de San Andrés, La Paz, Bolivia
| | - Jean-François Renno
- DIADE, Univ Montpellier, CIRAD, IRD, Montpellier, France
- Laboratoire Mixte International—Evolution et Domestication de l’Ichtyofaune Amazonienne (LMI—EDIA), IIAP, UAGRM, IRD, Paris, France
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Mariac C, Renno JF, Carmen Garcia-Davila, Vigouroux Y, Mejia E, Angulo C, Castro Ruiz D, Estivals G, Nolorbe C, García Vasquez A, Nuñez J, Cochonneau G, Flores M, Alvarado J, Vertiz J, Chota-Macuyama W, Sánchez H, Miranda G, Duponchelle F. Species-level ichthyoplankton dynamics for 97 fishes in two major river basins of the Amazon using quantitative metabarcoding. Mol Ecol 2021; 31:1627-1648. [PMID: 33949023 DOI: 10.1111/mec.15944] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Revised: 02/20/2021] [Accepted: 04/23/2021] [Indexed: 12/01/2022]
Abstract
The Amazon basin holds the world's largest freshwater fish diversity. Information on the intensity and timing of reproductive ecology of Amazonian fish is scant. We use a metabarcoding method by capture using a single probe to quantify species-level ichthyoplankton dynamics. We sampled the Marañón and the Ucayali rivers in Peru monthly for 2 years. We identified 97 species that spawned mainly during the flood start, the flood end or the receding periods, although some species had spawning activity in more than one period. This information was new for 40 of the species in the Amazon basin and 80 species in Peru. Most species ceased spawning for a month during a strong hydrological anomaly in January 2016, demonstrating the rapidity with which they react to environmental modifications during the breeding season. We also document another unreported event in the Amazon basin, the inverse phenology of species belonging to one genus (Triportheus). Overall larval flow in the Marañón was more than twice that of the Ucayali, including for most commercial species (between two and 20 times higher), whereas the Ucayali accounts for ~80% of the fisheries landings in the region. Our results are discussed in the light of the main anthropogenic threats to fishes, hydropower dam construction and the Hidrovía Amazónica, and should serve as a pre-impact baseline.
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Affiliation(s)
- Cédric Mariac
- DIADE, Univ Montpellier, CIRAD, IRD, Montpellier, France.,Laboratoire Mixte International - Evolution et Domestication de l'Ichtyofaune Amazonienne (LMI - EDIA), IIAP, UAGRM, IRD, Montpellier, France
| | - Jean-François Renno
- DIADE, Univ Montpellier, CIRAD, IRD, Montpellier, France.,Laboratoire Mixte International - Evolution et Domestication de l'Ichtyofaune Amazonienne (LMI - EDIA), IIAP, UAGRM, IRD, Montpellier, France
| | - Carmen Garcia-Davila
- Laboratoire Mixte International - Evolution et Domestication de l'Ichtyofaune Amazonienne (LMI - EDIA), IIAP, UAGRM, IRD, Montpellier, France.,Laboratorio de Biología y Genética Molecular (LBGM), Instituto de Investigaciones de la Amazonía Peruana (IIAP), Iquitos, Perú
| | - Yves Vigouroux
- DIADE, Univ Montpellier, CIRAD, IRD, Montpellier, France.,Laboratoire Mixte International - Evolution et Domestication de l'Ichtyofaune Amazonienne (LMI - EDIA), IIAP, UAGRM, IRD, Montpellier, France
| | - Eduardo Mejia
- Laboratoire Mixte International - Evolution et Domestication de l'Ichtyofaune Amazonienne (LMI - EDIA), IIAP, UAGRM, IRD, Montpellier, France.,Laboratorio de Biología y Genética Molecular (LBGM), Instituto de Investigaciones de la Amazonía Peruana (IIAP), Iquitos, Perú
| | - Carlos Angulo
- Laboratoire Mixte International - Evolution et Domestication de l'Ichtyofaune Amazonienne (LMI - EDIA), IIAP, UAGRM, IRD, Montpellier, France.,Laboratorio de Biología y Genética Molecular (LBGM), Instituto de Investigaciones de la Amazonía Peruana (IIAP), Iquitos, Perú
| | - Diana Castro Ruiz
- Laboratoire Mixte International - Evolution et Domestication de l'Ichtyofaune Amazonienne (LMI - EDIA), IIAP, UAGRM, IRD, Montpellier, France.,Laboratorio de Biología y Genética Molecular (LBGM), Instituto de Investigaciones de la Amazonía Peruana (IIAP), Iquitos, Perú
| | - Guillain Estivals
- Laboratoire Mixte International - Evolution et Domestication de l'Ichtyofaune Amazonienne (LMI - EDIA), IIAP, UAGRM, IRD, Montpellier, France.,Laboratorio de Biología y Genética Molecular (LBGM), Instituto de Investigaciones de la Amazonía Peruana (IIAP), Iquitos, Perú
| | - Christian Nolorbe
- Laboratoire Mixte International - Evolution et Domestication de l'Ichtyofaune Amazonienne (LMI - EDIA), IIAP, UAGRM, IRD, Montpellier, France.,Laboratorio de Biología y Genética Molecular (LBGM), Instituto de Investigaciones de la Amazonía Peruana (IIAP), Iquitos, Perú
| | - Aurea García Vasquez
- Laboratoire Mixte International - Evolution et Domestication de l'Ichtyofaune Amazonienne (LMI - EDIA), IIAP, UAGRM, IRD, Montpellier, France.,Laboratorio de Biología y Genética Molecular (LBGM), Instituto de Investigaciones de la Amazonía Peruana (IIAP), Iquitos, Perú
| | - Jesus Nuñez
- Laboratoire Mixte International - Evolution et Domestication de l'Ichtyofaune Amazonienne (LMI - EDIA), IIAP, UAGRM, IRD, Montpellier, France.,BOREA, MNHN, SU, UA, CNRS, IRD, Université de Caen-Normandie, France
| | | | - Mayra Flores
- Laboratoire Mixte International - Evolution et Domestication de l'Ichtyofaune Amazonienne (LMI - EDIA), IIAP, UAGRM, IRD, Montpellier, France.,Laboratorio de Biología y Genética Molecular (LBGM), Instituto de Investigaciones de la Amazonía Peruana (IIAP), Iquitos, Perú
| | - Jhon Alvarado
- Laboratoire Mixte International - Evolution et Domestication de l'Ichtyofaune Amazonienne (LMI - EDIA), IIAP, UAGRM, IRD, Montpellier, France.,Laboratorio de Biología y Genética Molecular (LBGM), Instituto de Investigaciones de la Amazonía Peruana (IIAP), Iquitos, Perú
| | - José Vertiz
- Laboratoire Mixte International - Evolution et Domestication de l'Ichtyofaune Amazonienne (LMI - EDIA), IIAP, UAGRM, IRD, Montpellier, France.,Laboratorio de Biología y Genética Molecular (LBGM), Instituto de Investigaciones de la Amazonía Peruana (IIAP), Iquitos, Perú
| | - Werner Chota-Macuyama
- Laboratoire Mixte International - Evolution et Domestication de l'Ichtyofaune Amazonienne (LMI - EDIA), IIAP, UAGRM, IRD, Montpellier, France.,Laboratorio de Biología y Genética Molecular (LBGM), Instituto de Investigaciones de la Amazonía Peruana (IIAP), Iquitos, Perú
| | - Homero Sánchez
- Laboratoire Mixte International - Evolution et Domestication de l'Ichtyofaune Amazonienne (LMI - EDIA), IIAP, UAGRM, IRD, Montpellier, France.,Laboratorio de Biología y Genética Molecular (LBGM), Instituto de Investigaciones de la Amazonía Peruana (IIAP), Iquitos, Perú
| | - Guido Miranda
- Laboratoire Mixte International - Evolution et Domestication de l'Ichtyofaune Amazonienne (LMI - EDIA), IIAP, UAGRM, IRD, Montpellier, France.,Wildlife Conservation Society, Bolivia Program, La Paz, Bolivia.,Unidad de Limnología, Instituto de Ecología, Universidad Mayor de San Andrés, La Paz, Bolivia
| | - Fabrice Duponchelle
- Laboratoire Mixte International - Evolution et Domestication de l'Ichtyofaune Amazonienne (LMI - EDIA), IIAP, UAGRM, IRD, Montpellier, France.,MARBEC, CNRS, Ifremer, IRD, Univ Montpellier, Montpellier, France
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