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Lima RC, de Lima SR, Rocha MS, Dos Anjos HDB, Dantas YCA, Benites IDN, Queiroz CDCS, Fraga EDC, Batista JDS. Identification of fish specimens of the Tocantins River, Brazil, using DNA barcoding. JOURNAL OF FISH BIOLOGY 2024; 104:1924-1939. [PMID: 38551122 DOI: 10.1111/jfb.15721] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/08/2023] [Revised: 12/03/2023] [Accepted: 02/25/2024] [Indexed: 06/27/2024]
Abstract
The fish fauna of the Tocantins River possesses many endemic species; however, it is little studied in molecular terms and is quite threatened by the construction of several hydroelectric dams. Therefore, the objective of this study was to identify the ichthyofauna of the Tocantins River using DNA barcoding. For this, collections were carried out in five points of this river, which resulted in the capture of 725 individuals from which partial sequences of the cytochrome oxidase subunit I (COI) gene were obtained for genetic analysis. A total of 443 haplotypes were recovered with the mean intraspecific K2P genetic distance of 1.82%. Altogether, 138 species were identified based on morphological criteria, which was a quantity that was much lower than that indicated by the four molecular methods (assemble species by automatic partitioning [ASAP], barcode index number [BIN], generalized mixed Yule coalescent (GMYC), and Bayesian Poisson tree processes [bPTP]) through which 152-157 molecular entities were identified. In all, 41 unique BINs were obtained based on the data generated in the BOLDSystems platform. According to the result indicated by ASAP (species delimitation approach considered the most appropriate in the present study), there was an increase of 17 molecular entities (12.32%), when compared to the number of species identified through their morphological criteria, as it can show cryptic diversity, candidates for new species, and misidentifications. There were 21 incongruities indicated between the different identification approaches for species. Therefore, it is suggested that these taxonomic problems be cautiously evaluated by experts to solve such taxonomic issues.
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Affiliation(s)
- Renato Corrêia Lima
- Programa de Pós-Graduação em Genética, Conservação e Biologia Evolutiva (PPG-GCBEv), Laboratório Temático de Biologia Molecular (LTBM), Instituto Nacional de Pesquisas da Amazônia (INPA), Manaus, Brazil
| | - Sabrina Rufino de Lima
- Programa de Pós-Graduação em Genética, Conservação e Biologia Evolutiva (PPG-GCBEv), Laboratório Temático de Biologia Molecular (LTBM), Instituto Nacional de Pesquisas da Amazônia (INPA), Manaus, Brazil
| | - Marcelo Salles Rocha
- Coordenação de Ciências Biológicas, Universidade do Estado do Amazonas (UEA), Manaus, Brazil
| | | | | | | | | | - Elmary da Costa Fraga
- Departamento de Química e Biologia, Universidade Estadual do Maranhão (UEMA), Caxias, Brazil
| | - Jacqueline da Silva Batista
- Coordenação de Biodiversidade (COBIO), Laboratório Temático de Biologia Molecular (LTBM), Programa de Pós-Graduação em Genética, Conservação e Biologia Evolutiva (PPG-GCBEv), Instituto Nacional de Pesquisas da Amazônia (INPA), Manaus, Brazil
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2
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Nascimento MHS, Birindelli JLO, Fraga E, Barros MC. Exploring hidden diversity: Molecular insights into the Leporinus species of the rivers of the Brazilian states of Maranhão and Piauí. JOURNAL OF FISH BIOLOGY 2024; 104:2056-2067. [PMID: 38590289 DOI: 10.1111/jfb.15753] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/24/2023] [Revised: 03/10/2024] [Accepted: 03/27/2024] [Indexed: 04/10/2024]
Abstract
The present study delved into the world of hidden diversity by examining specimens identified as Leporinus piau from the river basins of the northern Brazilian states of Maranhão and Piauí. Using genetic analyses that combined data from three mitochondrial markers and one nuclear marker, the study identified two well-supported groups, reinforcing the findings of previous publications. The first group, found in samples from the Itapecuru, Mearim, Turiaçu, and Pericumã basins, in Maranhão, appears to represent a relatively ancient diversification and the possibility of concealed cryptic diversity. The second group, comprising specimens from the Parnaíba (Piauí) and Mearim (Maranhão) basins, appears to have resulted from a more recent process of diversification and has a close relationship with Leporinus friderici from the type locality. Our findings not only confirm the existence of a complex scenario of cryptic diversity in the genus Leporinus from the study basins but also underscore the taxonomic inconsistencies within this group of fish. This study offers a comprehensive analysis of the species diversity of the Maranhão and Piauí basins, which are critical regions for the conservation of Amazonian fish, providing valuable insights for the sustainable management and conservation of these fish.
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Affiliation(s)
- Maria Histelle Sousa Nascimento
- Departamento de Desenvolvimento e Ensino, Instituto Federal de Educação, Ciência e Tecnologia do Maranhão, Caxias, Brazil
- Rede de Biodiversidade e Biotecnologia da Amazônia Legal, Universidade Federal do Maranhão, São Luis, Brazil
- Departamento de Química e Biologia, Universidade Estadual do Maranhão, Caxias, Brazil
| | | | - Elmary Fraga
- Departamento de Química e Biologia, Universidade Estadual do Maranhão, Caxias, Brazil
| | - Maria Claudene Barros
- Rede de Biodiversidade e Biotecnologia da Amazônia Legal, Universidade Federal do Maranhão, São Luis, Brazil
- Departamento de Química e Biologia, Universidade Estadual do Maranhão, Caxias, Brazil
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3
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Limeira Filho D, França ERDR, Costa DKDP, Lima RC, Nascimento MHSD, Batista JDS, Barros MC, Fraga EDC. Molecular Evidence Reveals Taxonomic Uncertainties and Cryptic Diversity in the Neotropical Catfish of the Genus Pimelodus (Siluriformes: Pimelodidae). BIOLOGY 2024; 13:162. [PMID: 38534432 DOI: 10.3390/biology13030162] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2024] [Revised: 02/22/2024] [Accepted: 02/28/2024] [Indexed: 03/28/2024]
Abstract
Pimelodus is the most speciose genus of the family Pimelodidae, and is amply distributed in the Neotropical region. The species-level taxonomy and phylogenetic relationships within this genus are still poorly resolved, however. These taxonomic problems and the general lack of data have generated major uncertainties with regard to the identification of specimens from different localities. In the present study, we applied a single-locus species delimitation approach to identify the MOTUs found within the genus Pimelodus and provide sound evidence for the evaluation of the species richness of this genus in the different river basins of the Neotropical region. The study was based on the analysis of sequences of the mitochondrial COI gene of 13 nominal species, which resulted in the identification of 24 consensus MOTUs. Only six nominal species were recovered as well-defined molecular entities by both the traditional barcoding analysis and the molecular delimitation methods, while the other seven presented cryptic diversity or persistent taxonomic uncertainties. The lineages identified from the Parnaíba ecoregions, Amazonas Estuary and Coastal Drainages may represent a much greater diversity of Pimelodus species than that recognized currently, although a more detailed study of this diversity will be necessary to provide a more definitive classification of the genus.
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Affiliation(s)
- Daniel Limeira Filho
- Graduate Program in Animal Science-PPGCA, Center of Agrarian Sciences-CCA, Maranhão State University-UEMA, São Luís 65055-310, MA, Brazil
| | - Elidy Rayane de Rezende França
- Graduate Program in Animal Science-PPGCA, Center of Agrarian Sciences-CCA, Maranhão State University-UEMA, São Luís 65055-310, MA, Brazil
| | - Dalton Kaynnan de Prado Costa
- Graduate Program in Biodiversity, Environment, and Health-PPGBAS, Caxias Center of Higher Education-CESC, Maranhão State University-UEMA, Praça Duque de Caxias, s/n-Morro do Alecrim, Centro, Caxias 65604-380, MA, Brazil
| | - Renato Correia Lima
- Graduate Program in Genetics, Conservation, and Evolutionary Biology (PPG-GCBEv), National Amazonian Research Institute-INPA, Av. André Araújo, 2936, Aleixo, Manaus 69060-001, AM, Brazil
| | - Maria Histelle Sousa do Nascimento
- Graduate Program in Biodiversity and Biotechnology-BIONORTE Network, Maranhão State University-UEMA, Cidade Universitária Paulo VI-Avenida Lourenço Vieira da Silva, n° 1.000, Jardim São Cristóvão, São Luís 665055-310, MA, Brazil
| | - Jacqueline da Silva Batista
- Graduate Program in Genetics, Conservation, and Evolutionary Biology (PPG-GCBEv), National Amazonian Research Institute-INPA, Av. André Araújo, 2936, Aleixo, Manaus 69060-001, AM, Brazil
- Molecular Biology Thematic Laboratory-LTBM, Coordination of Biodiversity-COBIO, National Amazonian Research Institute-INPA, Av. André Araújo, 2936, Petrópolis, Manaus 69067-375, AM, Brazil
| | - Maria Claudene Barros
- Graduate Program in Animal Science-PPGCA, Center of Agrarian Sciences-CCA, Maranhão State University-UEMA, São Luís 65055-310, MA, Brazil
- Graduate Program in Biodiversity, Environment, and Health-PPGBAS, Caxias Center of Higher Education-CESC, Maranhão State University-UEMA, Praça Duque de Caxias, s/n-Morro do Alecrim, Centro, Caxias 65604-380, MA, Brazil
- Graduate Program in Biodiversity and Biotechnology-BIONORTE Network, Maranhão State University-UEMA, Cidade Universitária Paulo VI-Avenida Lourenço Vieira da Silva, n° 1.000, Jardim São Cristóvão, São Luís 665055-310, MA, Brazil
- Laboratory of Molecular Biology-LABMOL, Department of Chemistry and Biology, Caxias Center of Higher Education-CESC, Maranhão State University-UEMA, Praça Duque de Caxias, s/n-Morro do Alecrim, Centro, Caxias 65604-380, MA, Brazil
| | - Elmary da Costa Fraga
- Graduate Program in Animal Science-PPGCA, Center of Agrarian Sciences-CCA, Maranhão State University-UEMA, São Luís 65055-310, MA, Brazil
- Graduate Program in Biodiversity, Environment, and Health-PPGBAS, Caxias Center of Higher Education-CESC, Maranhão State University-UEMA, Praça Duque de Caxias, s/n-Morro do Alecrim, Centro, Caxias 65604-380, MA, Brazil
- Laboratory of Genetics-LABGEN, Department of Chemistry and Biology, Caxias Center of Higher Education-CESC, Maranhão State University-UEMA, Praça Duque de Caxias, s/n-Morro do Alecrim, Centro, Caxias 65604-380, MA, Brazil
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4
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Ramirez JL, Machado CB, de Mello Affonso PRA, Galetti PM. Speciation in Coastal Basins Driven by Staggered Headwater Captures: Dispersal of a Species Complex, Leporinus bahiensis, as Revealed by Genome-wide SNP Data. Syst Biol 2023; 72:973-983. [PMID: 37260367 PMCID: PMC10627554 DOI: 10.1093/sysbio/syad034] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Revised: 05/22/2023] [Accepted: 05/30/2023] [Indexed: 06/02/2023] Open
Abstract
Past sea level changes and geological instability along watershed boundaries have largely influenced fish distribution across coastal basins, either by dispersal via palaeodrainages now submerged or by headwater captures, respectively. Accordingly, the South American Atlantic coast encompasses several small and isolated drainages that share a similar species composition, representing a suitable model to infer historical processes. Leporinus bahiensis is a freshwater fish species widespread along adjacent coastal basins over narrow continental shelf with no evidence of palaeodrainage connections at low sea level periods. Therefore, this study aimed to reconstruct its evolutionary history to infer the role of headwater captures in the dispersal process. To accomplish this, we employed molecular-level phylogenetic and population structure analyses based on Sanger sequences (5 genes) and genome-wide SNP data. Phylogenetic trees based on Sanger data were inconclusive, but SNPs data did support the monophyletic status of L. bahiensis. Both COI and SNP data revealed structured populations according to each hydrographic basin. Species delimitation analyses revealed from 3 (COI) to 5 (multilocus approach) MOTUs, corresponding to the sampled basins. An intricate biogeographic scenario was inferred and supported by Approximate Bayesian Computation (ABC) analysis. Specifically, a staggered pattern was revealed and characterized by sequential headwater captures from basins adjacent to upland drainages into small coastal basins at different periods. These headwater captures resulted in dispersal throughout contiguous coastal basins, followed by deep genetic divergence among lineages. To decipher such recent divergences, as herein represented by L. bahiensis populations, we used genome-wide SNPs data. Indeed, the combined use of genome-wide SNPs data and ABC method allowed us to reconstruct the evolutionary history and speciation of L. bahiensis. This framework might be useful in disentangling the diversification process in other neotropical fishes subject to a reticulate geological history.
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Affiliation(s)
- Jorge L Ramirez
- Facultad de Ciencias Biológicas, Universidad Nacional Mayor de San Marcos, Lima, Peru
- Museo de Historia Natural de la Universidad Nacional Mayor de San Marcos, Lima, Peru
| | - Carolina B Machado
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, SP, Brazil
| | | | - Pedro M Galetti
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, SP, Brazil
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Nascimento MHS, Aragão DG, Silva JLN, Lima RC, Birindelli JLO, Fraga EC, Barros MC. The DNA barcode reveals cryptic diversity and a new record for the genus Leporinus (Characiformes, Anostomidae) in the hydrographic basins of central northern Brazil. PeerJ 2023; 11:e15184. [PMID: 37250713 PMCID: PMC10225125 DOI: 10.7717/peerj.15184] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Accepted: 03/15/2023] [Indexed: 05/31/2023] Open
Abstract
Leporinus is one of the most speciose genera of the order Characiformes, with 81 valid species distributed throughout much of Central and South America. The considerable diversity of this genus has generated extensive debate on its classification and internal arrangement. In the present study, we investigated the species diversity of the genus Leporinus in central northern Brazil, and conclude that six valid species-Leporinus maculatus, Leporinus unitaeniatus, Leporinus affinis, Leporinus venerei, Leporinus cf. friderici, and Leporinus piau-are found in the hydrographic basins of the Brazilian states of Maranhão, Piauí, and Tocantins. We analyzed 182 sequences of the Cytochrome Oxidase subunit I gene, of which, 157 were obtained from Leporinus specimens collected from the basins of the Itapecuru, Mearim, Turiaçu, Pericumã, Periá, Preguiças, Parnaíba, and Tocantins rivers. The species delimitation analyses, based on the ABGD, ASAP, mPTP, bPTP, and GMYC methods, revealed the presence of four distinct molecular operational taxonomic units (MOTUs), identified as L. maculatus, L. unitaeniatus, L. affinis, and L. piau (from the Parnaíba River). The bPTP method restricted L. venerei to a single MOTU, and confirmed the occurrence of this species in the rivers of Maranhão for the first time. The separation of L. cf. friderici into two clades and the subsequent formation of different operational taxonomic units was consistent with polyphyly in this species, which indicates the existence of cryptic diversity. The arrangement of L. cf. friderici and L. piau in two different clades supports the conclusion that the L. piau specimens from Maranhão were misidentified, based on their morphological traits, reflecting the taxonomic inconsistencies that exist among morphologically similar species. Overall, then, the species delimitation methods employed in the present study indicated the presence of six MOTUs-L. maculatus, L. unitaenitus, L. affinis, L. cf. friderici, L. venerei, and L. piau. In the case of two other MOTUs identified in the present study, one (L. venerei) is a new record for the state of Maranhão, and we believe that the other represents a population of L. piau from the basin of the Parnaíba River.
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Affiliation(s)
- Maria Histelle Sousa Nascimento
- Department of Chemistry and Biology, Maranhão State University, Caxias, Maranhão, Brazil
- Graduate Network Program in the Biodiversity and Biotechnology of Legal Amazonia, Biological Sciences Institute, Belem, Pará, Brazil
| | - Deborah Gaído Aragão
- Department of Chemistry and Biology, Maranhão State University, Caxias, Maranhão, Brazil
| | | | - Renato Correia Lima
- Graduate Program in Genetics, Conservation, and Evolutionary Biology, National Amazonian Research Institute, Manaus, Amazonas, Brazil
| | | | - Elmary Costa Fraga
- Department of Chemistry and Biology, Maranhão State University, Caxias, Maranhão, Brazil
| | - Maria Claudene Barros
- Department of Chemistry and Biology, Maranhão State University, Caxias, Maranhão, Brazil
- Graduate Network Program in the Biodiversity and Biotechnology of Legal Amazonia, Biological Sciences Institute, Belem, Pará, Brazil
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6
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Rizo-Fuentes MA, Correa-Cárdenas CA, Lasso CA, Morales-Betancourt MA, Barragán-Barrera DC, Caballero S. Phylogeography, genetic diversity and population structure of the freshwater stingray, Paratrygon aiereba (Müller & Henle, 1841) (Myliobatiformes: Potamotrygonidae) in the Colombian Amazon and Orinoco basins. Mitochondrial DNA A DNA Mapp Seq Anal 2020; 32:20-33. [PMID: 33346684 DOI: 10.1080/24701394.2020.1844679] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
The freshwater stingray Paratrygon aiereba have coloration, osteological and morphometric variations that could suggest the existence of more than one species in Colombia. In order to evaluate the phylogeography, population structure and genetic diversity for P. aiereba distributed in the Amazon and Orinoco basins, we amplified Cytochrome oxidase subunit 1 (COI) partial region of mitochondrial DNA (mtDNA) in 50 samples from eight different sub-basins. Our results suggest three phylogroups and a vicariance event occurred 43 million years ago proposing how Paratrygon diverged into the basins. A high population structure (ΦST = 0.692; p < 0.005) and a value of (K) of 3 were defined. A high genetic diversity within phylogroups was found: Phylogroup A (h = 0.64; π% = 2.48), Phylogroup B (h = 0.552; π% = 1.67), and Phylogroup C (h = 0.49; π% = 0.73). These results should be considered in local management plans, conservation programs and reclassification in at least Amazon and Orinoco.
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Affiliation(s)
- Maira A Rizo-Fuentes
- Laboratorio de Ecología Molecular de Vertebrados Acuáticos (LEMVA), Departamento de Ciencias Biológicas, Universidad de los Andes, Bogotá, Colombia.,Programa de Biología, Departamento de Ciencias Básicas, Universidad de La Salle, Bogotá, Colombia
| | - Camilo A Correa-Cárdenas
- Programa de Biología, Departamento de Ciencias Básicas, Universidad de La Salle, Bogotá, Colombia.,Grupo de Investigación en Enfermedades Tropicales del Ejército (GINETEJ), Laboratorio de Referencia e Investigación, Dirección de Sanidad Ejército, Bogotá, Colombia
| | - Carlos A Lasso
- Programa Biología de la Conservación y Uso de la Biodiversidad, Instituto de Investigación de Recursos Biológicos Alexander Von Humboldt, Bogotá, Colombia
| | - Mónica A Morales-Betancourt
- Programa Biología de la Conservación y Uso de la Biodiversidad, Instituto de Investigación de Recursos Biológicos Alexander Von Humboldt, Bogotá, Colombia
| | - Dalia C Barragán-Barrera
- Laboratorio de Ecología Molecular de Vertebrados Acuáticos (LEMVA), Departamento de Ciencias Biológicas, Universidad de los Andes, Bogotá, Colombia.,Centro de Investigaciones Oceanográficas e Hidrográficas del Caribe (CIOH), Dirección General Marítima (DIMAR), Cartagena de Indias, Colombia
| | - Susana Caballero
- Laboratorio de Ecología Molecular de Vertebrados Acuáticos (LEMVA), Departamento de Ciencias Biológicas, Universidad de los Andes, Bogotá, Colombia
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7
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Molecular phylogeny and species delimitation of the genus Schizodon (Characiformes, Anostomidae). Mol Phylogenet Evol 2020; 153:106959. [PMID: 32920128 DOI: 10.1016/j.ympev.2020.106959] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2019] [Revised: 07/16/2020] [Accepted: 08/13/2020] [Indexed: 11/23/2022]
Abstract
The genus Schizodon is part of a group of headstanders and relatives (Family Anostomidae) that are widespread and ecologically important fishes in South American rivers. Schizodon includes 15 nominal species but their taxonomy has been challenging due to paucity of decisive characters to diagnose species. We present new molecular data to assess species boundaries or molecular operational taxonomic units (MOTUs), and to infer phylogenetic relationships among species. Evidence from two mitochondrial and three nuclear genes was used in these analyses. Mitochondrial DNA data for 112 specimens (from 11 nominal species) supported 13 consensus MOTUs, six of which matched valid nominal species (Schizodon borellii, S. fasciatus, S. intermedius, S. isognathus, S. knerii and S. scotorhabdotus). The nominal species Schizodon vittatus, S. nasutus, and S. dissimilis were subdivided into two MOTUs each, revealing either cryptic species or strong population structuring. In contrast, S. platae and S. jacuiensis constituted a single MOTU, indicating a possible case of synonymy. Our phylogenetic analysis subdivided the genus Schizodon into two large clades that are compatible with observed color patterns and biogeographic distribution. The first clade includes species with three to four conspicuous dark vertical bars on the flanks that originated in the Amazonas region (S. borellii, S. dissimilis, S. intermedius, S. fasciatus, S. scotorhabdotus, S. vittatus, and a cryptic species, Schizodon aff. vittatus). The second clade includes species with a conspicuous dark caudal blotch on the caudal peduncle, with vertical bars absent or inconspicuous, with a biogeographic origin in the La Plata drainage (S. isognathus, S. jacuiensis, S. knerii, S. nasutus and S. platae). Our results reinforce the importance of using molecular analyses to accelerate the study of diversity, particularly in groups with a wide distribution, few variable meristic characters, and high morphological plasticity, which may hide still unknown or underestimated diversity.
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8
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Hidden diversity in Prochilodus nigricans: A new genetic lineage within the Tapajós River basin. PLoS One 2020; 15:e0237916. [PMID: 32842138 PMCID: PMC7447553 DOI: 10.1371/journal.pone.0237916] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2020] [Accepted: 08/06/2020] [Indexed: 11/23/2022] Open
Abstract
Highly spread through the Amazon River basin, Prochilodus nigricans have had its taxonomic validity recently questioned, when genetic differences between Western and Eastern Amazon populations from the Brazilian shield were detected. This area has been seeing as a region of high ichthyofaunal diversity and endemism, in which the hybrid origin of the Tapajós River basin has been raised. In this paper, we report a new molecular lineage within P. nigricans of Tapajós River, highlighting this region still hides taxonomically significant diversity. Haplotype networks were reconstructed using the mitochondrial COI and ATP6/8 markers, which were also used to calculate genetic distances among clusters. We additionally conducted a delimiting species approach by employing a Generalized Mixed Yule-Coalescent model (GMYC) with COI sequences produced here, and previous ones published for individuals sampled across the Amazon River basin. In addition to the genetic differentiation within P. nigricans, our findings favor the hypothesis of hybrid origin of the Tapajós River basin and reaffirm the importance of studies aiming to investigate hidden diversity to address taxonomic and biogeographic issues, that certainly benefit better biodiversity conservation actions.
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9
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Hardulak LA, Morinière J, Hausmann A, Hendrich L, Schmidt S, Doczkal D, Müller J, Hebert PDN, Haszprunar G. DNA metabarcoding for biodiversity monitoring in a national park: Screening for invasive and pest species. Mol Ecol Resour 2020; 20:1542-1557. [PMID: 32559020 DOI: 10.1111/1755-0998.13212] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2019] [Revised: 06/03/2020] [Accepted: 06/09/2020] [Indexed: 01/09/2023]
Abstract
DNA metabarcoding was utilized for a large-scale, multiyear assessment of biodiversity in Malaise trap collections from the Bavarian Forest National Park (Germany, Bavaria). Principal component analysis of read count-based biodiversities revealed clustering in concordance with whether collection sites were located inside or outside of the National Park. Jaccard distance matrices of the presences of barcode index numbers (BINs) at collection sites in the two survey years (2016 and 2018) were significantly correlated. Overall similar patterns in the presence of total arthropod BINs, as well as BINs belonging to four major arthropod orders across the study area, were observed in both survey years, and are also comparable with results of a previous study based on DNA barcoding of Sanger-sequenced specimens. A custom reference sequence library was assembled from publicly available data to screen for pest or invasive arthropods among the specimens or from the preservative ethanol. A single 98.6% match to the invasive bark beetle Ips duplicatus was detected in an ethanol sample. This species has not previously been detected in the National Park.
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Affiliation(s)
- Laura A Hardulak
- SNSB-Zoologische Staatssammlung München, Munich, Germany.,Ludwig-Maximilians-Universität München, Munich, Germany
| | | | - Axel Hausmann
- SNSB-Zoologische Staatssammlung München, Munich, Germany
| | - Lars Hendrich
- SNSB-Zoologische Staatssammlung München, Munich, Germany
| | - Stefan Schmidt
- SNSB-Zoologische Staatssammlung München, Munich, Germany
| | - Dieter Doczkal
- SNSB-Zoologische Staatssammlung München, Munich, Germany
| | - Jörg Müller
- National Park Bavarian Forest, Grafenau, Germany.,Field Station Fabrikschleichach, Department of Animal Ecology and Tropical Biology, University of Würzburg, Biocenter, Rauhenebrach, Germany
| | - Paul D N Hebert
- Centre for Biodiversity Genomics, University of Guelph, Guelph, ON, Canada
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10
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Arruda PSS, Ferreira DC, Oliveira C, Venere PC. DNA Barcoding Reveals High Levels of Divergence among Mitochondrial Lineages of Brycon (Characiformes, Bryconidae). Genes (Basel) 2019; 10:genes10090639. [PMID: 31450860 PMCID: PMC6769914 DOI: 10.3390/genes10090639] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2019] [Revised: 08/20/2019] [Accepted: 08/21/2019] [Indexed: 02/02/2023] Open
Abstract
Brycon is an important group of Neotropical fish and the principal genus of the family Bryconidae, with 44 valid species that are found in some Central American rivers and practically all the major hydrographic basins of South America. These fish are medium to large in size, migratory, omnivorous, important seed dispersers for riparian forests, and bioindicators of environmental quality, given that they are found preferentially in rivers with clean, well oxygenated water. Many Brycon species are important fishery resources and some are farmed. Morphological and molecular studies have nevertheless indicated that the group is not monophyletic and has a number of unresolved taxonomic problems. Given this, the present study aimed to identify the Molecular Operational Taxonomic Units (MOTUs) of the genus using the mitochondrial cytochrome c oxidase I (COI) gene, with analyses of genetics distance (NJ), maximum likelihood (ML), and Bayesian Inference (BI), combined with two different species delimitation approaches (GMYC and ABGD). The results indicate that at least 31 MOTUs exist within the 18 species identified a priori based on their morphology. Many of these lineages require further investigation for a more definitive classification.
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Affiliation(s)
- Pábila S S Arruda
- Programa de Pós-Graduação em Ecologia e Conservação da Biodiversidade, Instituto de Biociências, Universidade Federal de Mato Grosso, Avenida Fernando Correia da Costa, 2367, Cuiabá, Mato Grosso 78060-900, Brazil
| | - Daniela C Ferreira
- Departamento de Biologia e Zoologia, Instituto de Biociências, Universidade Federal de Mato Grosso, Avenida Fernando Correia da Costa, 2367, Cuiabá, Mato Grosso 78060-900, Brazil
| | - Claudio Oliveira
- Departamento de Morfologia, Instituto de Biociências, Universidade Estadual Paulista Júlio de Mesquita Filho - UNESP, Rubião Jr S-N, Botucatu, São Paulo 18618-970, Brazil
| | - Paulo C Venere
- Departamento de Biologia e Zoologia, Instituto de Biociências, Universidade Federal de Mato Grosso, Avenida Fernando Correia da Costa, 2367, Cuiabá, Mato Grosso 78060-900, Brazil.
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Santos EOD, Deon GA, Almeida RBD, Oliveira EAD, Nogaroto V, Silva HPD, Pavanelli CS, Cestari MM, Bertollo LAC, Moreira-Filho O, Vicari MR. Cytogenetics and DNA barcode reveal an undescribed Apareiodon species (Characiformes: Parodontidae). Genet Mol Biol 2019; 42:365-373. [PMID: 31259363 PMCID: PMC6726146 DOI: 10.1590/1678-4685-gmb-2018-0066] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2018] [Accepted: 08/01/2018] [Indexed: 11/22/2022] Open
Abstract
Parodontidae is a small group of fish and some species are particularly difficult
to identify due to the lack of sufficiently consistent morphological traits.
Cytogenetically, the species possess 2n = 54 chromosomes and are either
sex-homomorphic or sex-heteromorphic (regarding its chromosomes). We evaluated
data on color, tooth morphology, cytogenetics, and mitochondrial markers (COI)
in Apareiodon specimens from the Aripuanã River (Amazon basin)
and the results were compared to other congeneric taxa. Morphological results
show an overlap of body color and tooth morphology to other known
Apareiodon. The cytogenetics data showed that the 2n = 54
chromosomes, 50 m/sm + 4 st and, a ZZ/ZW sex chromosome system in
Apareiodon sp. are common to other species of the genus.
However, the number and chromosomal localization of the 45S ribosomal and
pPh2004 satellite DNA sites, in addition to W chromosome
localization of the pPh2004 appear to be exclusive cytogenetic
features in Apareiodon sp. Our phylogenetic tree revealed
well-supported clades and confirmed, by barcode species delimitation analysis, a
new Molecular Operational Taxonomic Unit (MOTU) for Apareiodon
sp. (Aripuanã River). As a whole, the above features support the occurrence of a
new species of the Apareiodon, thus far unknown for the
Parodontidae.
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Affiliation(s)
- Emanoel Oliveira Dos Santos
- Departamento de Genética, Programa de Pós-Graduação em Genética, Universidade Federal do Paraná, Curitiba, PR, Brazil
| | - Geize Aparecida Deon
- Departamento de Biologia Estrutural, Molecular e Genética, Universidade Estadual de Ponta Grossa, Ponta Grossa, PR, Brazil
| | - Rafael Bonfim de Almeida
- Departamento de Genética, Programa de Pós-Graduação em Genética, Universidade Federal do Paraná, Curitiba, PR, Brazil
| | | | - Viviane Nogaroto
- Departamento de Biologia Estrutural, Molecular e Genética, Universidade Estadual de Ponta Grossa, Ponta Grossa, PR, Brazil
| | - Hugmar Pains da Silva
- Laboratório de Citogenética e Genética Animal, Instituto de Biociências, Universidade Federal de Mato Grosso, Cuiabá, MT, Brazil
| | - Carla Simone Pavanelli
- Núcleo de Pesquisas em Limnologia, Ictiologia e Aquicultura (Nupélia), Universidade Estadual de Maringá, Maringá, PR, Brazil
| | - Marta Margarete Cestari
- Departamento de Genética, Programa de Pós-Graduação em Genética, Universidade Federal do Paraná, Curitiba, PR, Brazil
| | | | - Orlando Moreira-Filho
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, São Paulo, SP, Brazil
| | - Marcelo Ricardo Vicari
- Departamento de Genética, Programa de Pós-Graduação em Genética, Universidade Federal do Paraná, Curitiba, PR, Brazil.,Departamento de Biologia Estrutural, Molecular e Genética, Universidade Estadual de Ponta Grossa, Ponta Grossa, PR, Brazil
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12
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Dagosta FC, Pinna MD. The Fishes of the Amazon: Distribution and Biogeographical Patterns, with a Comprehensive List of Species. BULLETIN OF THE AMERICAN MUSEUM OF NATURAL HISTORY 2019. [DOI: 10.1206/0003-0090.431.1.1] [Citation(s) in RCA: 109] [Impact Index Per Article: 21.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Affiliation(s)
- Fernando C.P. Dagosta
- Universidade Federal da Grande Dourados Faculdade de Ciências Biológicas e Ambientais Dourados, Mato Grosso do Sul, Brazil
| | - Mário De Pinna
- Museu de Zoologia da Universidade de São Paulo São Paulo, Brazil
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