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de Morais VIB, de Oliveira JVL, Alesci A, de Almeida MC, Artoni RF. Exploring Chromosomal Polymorphism and Evolutionary Implications in Rineloricaria lanceolata (Günther, 1868) (Siluriformes: Loricariidae): Insights from Meiotic Behavior and Phylogenetic Analysis. BIOLOGY 2024; 13:708. [PMID: 39336135 PMCID: PMC11428316 DOI: 10.3390/biology13090708] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/06/2024] [Revised: 09/03/2024] [Accepted: 09/04/2024] [Indexed: 09/30/2024]
Abstract
Chromosomal polymorphism is a significant aspect of population genetics, influencing the adaptation and evolution of species. In Rineloricaria lanceolata, a Neotropical fish species, chromosomal polymorphism has been observed, yet the underlying mechanisms and evolutionary implications remain poorly understood. This article aims to investigate the chromosomal polymorphism in Rineloricaria lanceolata, focusing on elucidating the meiotic behavior of karyotypic variants and tracing the phylogenetic origins of this polymorphism within the genus. By employing molecular markers and cytogenetic techniques, we aim to uncover the mechanisms driving chromosomal rearrangements and their potential role in speciation and adaptation. Understanding the genetic basis of chromosomal polymorphism in R. lanceolata not only contributes to our knowledge of species evolution but also holds implications for the conservation of genetic diversity within this vulnerable group of Neotropical fishes.
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Affiliation(s)
| | | | - Alessio Alesci
- Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, University of Messina, 98166 Messina, Italy
| | - Mara Cristina de Almeida
- Department of Structural and Molecular Biology and Genetic, State University of Ponta Grossa, Ponta Grossa 84030-900, PR, Brazil
| | - Roberto Ferreira Artoni
- Department of Structural and Molecular Biology and Genetic, State University of Ponta Grossa, Ponta Grossa 84030-900, PR, Brazil
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Mejia E, Buckup PA. Species boundaries of the whiptail catfish Rineloricaria (Siluriformes: Loricariidae) from the Paraíba do Sul River drainage, southeastern Brazil, with species redescriptions and description of a new species. JOURNAL OF FISH BIOLOGY 2024; 105:288-313. [PMID: 38747127 DOI: 10.1111/jfb.15780] [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: 01/17/2024] [Revised: 04/13/2024] [Accepted: 04/17/2024] [Indexed: 07/19/2024]
Abstract
Species of the catfish genus Rineloricaria are common in the Paraíba do Sul River basin, in southeastern Brazil; here we present a revision of the taxonomic diversity and geographic distribution of the species of the genus inhabiting the basin, based on novel morphologic and molecular data. Five species delimitation methods based on cytochrome C oxidase subunit 1 nucleotide sequences yielded comparable molecular operational taxonomic units. The automatic barcode gap discovery, assemble species by automatic partitioning, barcode index number, and Bayesian implementation of the Poisson tree process methods supported the recognition of five evolutionary lineages. These taxonomic units were assigned to the previously described Rineloricaria nigricauda, Rineloricaria steindachneri, Rineloricaria zawadzkii, and Rineloricaria nudipectoris, and an additional undescribed species. R. zawadzkii was further divided into two intraspecific geographically structured lineages using the generalized mixed Yule coalescent delimitation method. A maximum likelihood phylogenetic analysis revealed that the five lineages from the Paraíba do Sul have closer relationships to different species from southern and southeastern Brazil (Ribeira de Iguape, Lagoa dos Patos, Uruguay, Paraguay, and Parana river basins) than to each other. Based on the analysis of lectotypes, recently collected material, and specimens from ichthyological collections, the poorly described R. nigricauda and R. steindachneri are redescribed following current descriptive standards. The undescribed species from the middle and upper Paraíba do Sul River basin is formally described. The description of a new species, along with the description of species boundaries in R. nigricauda and R. steindachneri, contributes to the knowledge of the ichthyofauna of the Paraíba do Sul River basin and adjacent coastal drainages of southeastern Brazil. An identification key for the species of Rineloricaria occurring in the Paraíba do Sul River basin is provided.
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Affiliation(s)
- Eduardo Mejia
- Programa de Pós-graduação em Ciências Biológicas (Zoologia), Museu Nacional, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Paulo A Buckup
- Programa de Pós-graduação em Ciências Biológicas (Zoologia), Museu Nacional, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
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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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Ramirez JL, Valdivia P, Rosas-Puchuri U, Valdivia NL. SPdel: A pipeline to compare and visualize species delimitation methods for single-locus datasets. Mol Ecol Resour 2023; 23:1959-1965. [PMID: 37702121 DOI: 10.1111/1755-0998.13864] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Revised: 07/28/2023] [Accepted: 08/30/2023] [Indexed: 09/14/2023]
Abstract
An accurate species delimitation is critical for biological studies. In this context, the use of molecular techniques along with species delimitation methods would help to a rapid and accurate biodiversity assessment. The species delimitation methods cluster data sets of orthologous sequences in molecular operational taxonomic units (MOTU). In particular, the methods based on a single gene are easily integrated with the widely used DNA barcoding approach. We developed SPdel a user-friendly pipeline to integrate different single-gene species delimitation methods. SPdel is designed to calculate and compare MOTUs obtained by different species delimitation approaches. SPdel also outputs diverse ready-to-publish quality figures, that facilitate the interpretation of results. SPdel aims to help researchers use species delimitation methods that would improve biodiversity studies.
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Affiliation(s)
- Jorge L Ramirez
- Facultad de Ciencias Biológicas, Universidad Nacional Mayor de San Marcos, Lima, Peru
| | - Paola Valdivia
- Department of Biology, The University of Oklahoma, Norman, Oklahoma, USA
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Urbano-Bonilla A, Londoño-Burbano A, Carvalho TP. A new species of rheophilic armored catfish of Rineloricaria (Siluriformes: Loricariidae) from the Vaupés River, Amazonas basin, Colombia. JOURNAL OF FISH BIOLOGY 2023; 103:1073-1084. [PMID: 37427785 DOI: 10.1111/jfb.15500] [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: 03/30/2023] [Revised: 07/04/2023] [Accepted: 07/05/2023] [Indexed: 07/11/2023]
Abstract
A new rheophilic species of the genus Rineloricaria is described for the Amazon basin in Colombia. Rineloricaria cachivera n. sp. differs from its congeners by having anterior to the first predorsal plate, an inconspicuous saddle-like mark; the presence of dark, diffuse blotches, present as unified dark colouration along most of the dorsal portion of the head, without bands or spots on the head; a long snout that occupies more than half the head length (HL), between 58.0% and 66.3% HL; a naked portion on the cleithral area from the border of lower lip reaching the origin of pectoral fin; and by having five series of lateral plates in longitudinal rows below the dorsal fin. The new species is morphologically similar to Rineloricaria daraha; however, it can be distinguished by the presence of six branched pectoral fin rays (vs. seven) and the lower lip surface with short thick papillae (vs. long finger papillae). An identification key to the Rineloricaria species of the Amazon River basin in Colombia is provided. The new species is herein categorized as Least Concern, following the IUCN criteria.
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Affiliation(s)
- Alexander Urbano-Bonilla
- Departamento de Biología, Facultad de Ciencias, Laboratorio de Ictiología, Pontificia Universidad Javeriana, Bogotá, Colombia
| | - Alejandro Londoño-Burbano
- Departamento de Vertebrados, Universidade Federal do Rio de Janeiro, Museu Nacional, Setor de Ictiologia Quinta da Boa Vista, Rio de Janeiro, Brazil
| | - Tiago P Carvalho
- Departamento de Biología, Facultad de Ciencias, Laboratorio de Ictiología, Pontificia Universidad Javeriana, Bogotá, Colombia
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Cortés-Hernández MÁ, López-Castaño JA, Milani N, DoNascimiento C. A new cryptic species of Imparfinis (Siluriformes: Heptapteridae) from the Orinoco River basin, revealed by an iterative approach. JOURNAL OF FISH BIOLOGY 2023; 103:1015-1030. [PMID: 37395669 DOI: 10.1111/jfb.15495] [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: 04/17/2023] [Revised: 06/26/2023] [Accepted: 06/29/2023] [Indexed: 07/04/2023]
Abstract
An iterative analysis of Imparfinis, combining phylogenetic analysis based on cytochrome oxidase gene and multivariate morphometrics, revealed a new cryptic species from the Andean tributaries of the Orinoco River basin, which is described here. The new species is sister to a clade constituted by Imparfinis hasemani and Imparfinis pijpersi, both from the river basins of the Guiana Shield, being also the most geographically proximate species. Nonetheless, the new species is most similar in general appearance to Imparfinis guttatus from the Madeira and Paraguay River drainages, being almost undistinguishable by conventional characters of external morphology, differing only by morphometric attributes overall. The new species can be distinguished from the remaining congeners by a unique combination of characters, including lower lobe of caudal fin darker than upper lobe, maxillary barbel reaching or surpassing pelvic-fin insertion, 12-15 gill rakers on first gill arch, 40-42 total vertebrae and 9-10 ribs. The new species constitutes the only representative from the Orinoco River basin belonging to Imparfinis sensu stricto.
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Affiliation(s)
- Miguel Ángel Cortés-Hernández
- Grupo de Investigación Evaluación, Manejo y Conservación de Recursos Hidrobiológicos y Pesqueros, Universidad de los Llanos, Villavicencio, Colombia
- Museo de Historia Natural de la Universidad de los Llanos, Villavicencio, Colombia
- Grupo de Investigación Cuencas, Fundación Neotropical Cuencas, Arauca, Colombia
| | - Jeisson Alexis López-Castaño
- Grupo de Investigación Evaluación, Manejo y Conservación de Recursos Hidrobiológicos y Pesqueros, Universidad de los Llanos, Villavicencio, Colombia
| | - Nadia Milani
- Centro Museo de Biología, Instituto de Zoología y Ecología Tropical, Facultad de Ciencias, Universidad Central de Venezuela, Caracas, Venezuela
| | - Carlos DoNascimiento
- Grupo de Ictiología, Instituto de Biología, Universidad de Antioquia, Medellín, Colombia
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Müller MI, Morais DH, da Costa LFST, de Vasconcelos Melo FT, Giese EG, Ávila RW, da Silva RJ. Revisiting the taxonomy of Rhabdias fuelleborni Travassos, 1928 (Nematoda, Rhabdiasidae) with approaches to delimitation of species and notes on molecular phylogeny. Parasitol Int 2023; 92:102692. [DOI: 10.1016/j.parint.2022.102692] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Revised: 10/11/2022] [Accepted: 10/14/2022] [Indexed: 11/06/2022]
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Gavazzoni M, Pavanelli CS, Graça WJ, De Oliveira EA, Moreira-Filho O, Margarido VP. Species delimitation in Psalidodon fasciatus (Cuvier, 1819) complex (Teleostei: Characidae) from three hydrographic basins. Biol J Linn Soc Lond 2022. [DOI: 10.1093/biolinnean/blac139] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
Abstract
Psalidodon fasciatus is a complex of several fish species widely distributed in Brazilian hydrographic systems that share morphological characteristics and show a high taxonomic complexity and genetic variability. Cytogenetic and molecular analyses were carried out in populations from three Brazilian hydrographic basins, aiming to contribute to systematic and biogeographical knowledge of the group. The chromosomal markers verified the occurrence of species-specific characters and indicated the existence of six distinct operational taxonomic units (OTUs): P. fasciatus (São Francisco River basin), Psalidodon sp. 1, Psalidodon sp. 2 and Psalidodon eigenmanniorum (Uruguay River basin); and Psalidodon sp. 3 and Psalidodon sp. 4 (Paraná River basin). The chromosomal markers showed more similarities among species from the Uruguay River and São Francisco River basins. DNA barcoding analyses (assemble species by automatic partitioning, neighbour-joining, maximum likelihood and maximum parsimony) indicated the existence of at least three distinct OTUs. The chromosomal evolution rates were demonstrated to be higher than the molecular evolution rates, reinforcing the importance of using chromosomal markers to delimit OTUs in integrative taxonomy studies. These results suggest that the São Francisco River Basin population (the type locality) should be considered as true P. fasciatus, and the others, until now treated as Psalidodon aff. fasciatus, are cryptic species.
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Affiliation(s)
- Mariane Gavazzoni
- Centro de Ciências Biológicas e da Saúde, Universidade Estadual do Oeste do Paraná , Cascavel, Paraná , Brazil
- Pós-graduação em Biologia Comparada, Centro de Ciências Biológicas, Universidade Estadual de Maringá , Maringá, Paraná , Brazil
| | - Carla S Pavanelli
- Pós-graduação em Biologia Comparada, Centro de Ciências Biológicas, Universidade Estadual de Maringá , Maringá, Paraná , Brazil
- Núcleo de Pesquisas em Limnologia, Ictiologia e Aquicultura (Nupélia), Centro de Ciências Biológicas, Universidade Estadual de Maringá , Maringá, Paraná , Brazil
| | - Weferson J Graça
- Pós-graduação em Biologia Comparada, Centro de Ciências Biológicas, Universidade Estadual de Maringá , Maringá, Paraná , Brazil
- Núcleo de Pesquisas em Limnologia, Ictiologia e Aquicultura (Nupélia), Centro de Ciências Biológicas, Universidade Estadual de Maringá , Maringá, Paraná , Brazil
- Departamento de Biologia, Centro de Ciências Biológicas, Universidade Estadual de Maringá , Maringá, Paraná , Brazil
| | - Ezequiel A De Oliveira
- Secretaria de Estado de Educação do Mato Grosso, São Felix do Araguaia , Mato Grosso , Brazil
| | - Orlando Moreira-Filho
- Departamento de Genética e Evolução, Universidade Federal de São Carlos , São Carlos, São Paulo , Brazil
| | - Vladimir P Margarido
- Centro de Ciências Biológicas e da Saúde, Universidade Estadual do Oeste do Paraná , Cascavel, Paraná , Brazil
- Pós-graduação em Biologia Comparada, Centro de Ciências Biológicas, Universidade Estadual de Maringá , Maringá, Paraná , Brazil
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Mendoza‐Ramírez BH, Páiz‐Medina L, Salvatierra‐Suárez T, Hernández N, Huete‐Pérez JA. A survey of aquatic macroinvertebrates in a river from the dry corridor of Nicaragua using biological indices and DNA barcoding. Ecol Evol 2022; 12:e9487. [PMID: 36349251 PMCID: PMC9636505 DOI: 10.1002/ece3.9487] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Revised: 08/31/2022] [Accepted: 10/17/2022] [Indexed: 11/07/2022] Open
Abstract
Aquatic macroinvertebrates are widely used as indicators for water quality assessment around the world. Modern strategies for environmental assessment implement molecular analysis to delimitate species of aquatic macroinvertebrates. Delimitation methods have been established to determine boundaries between species units using sequencing data from DNA barcodes and serve as first exploratory tools for taxonomic revisions. This is useful in regions such as the neotropics where aquatic macroinvertebrate habitats are threatened by human interference and DNA databases remain understudied. We asked whether the biodiversity of aquatic macroinvertebrates in a stream in Nicaragua, within the Central American Dry Corridor, could be characterized with biological indices and DNA barcoding. In this study, we combined regional biological indices (BMWP-CR, IBF-SV-2010) along with distance-based (ASAP, BIN) and tree-based (GMYC, bPTP) delimitation methods, as well as nucleotide BLAST in public barcode databases. We collected samples from the upper, middle, and low reaches of the Petaquilla river. The three sites presented excellent water quality with the BMWP-CR index, but evidence of high organic pollution was found in the middle reach with the IBF-SV-2010 index. We report a total of 219 COI sequences successfully generated from 18 families and 8 orders. Operational taxonomic units (OTUs) designation ranged from 69 to 73 using the four methods, with a congruency of 92% for barcode assignation. Nucleotide BLAST identified 14 species (27.4% of barcodes) and 33 genera (39.3% of barcodes) from query sequences in GenBank and BOLD system databases. This small number of identified OTUs may be explained by the paucity of molecular data from the Neotropical region. Our study provides valuable information about the characterization of macroinvertebrate families that are important biological indicators for the assessment of water quality in Nicaragua. The application of molecular approaches will allow the study of local diversity and further improve the application of molecular techniques for biomonitoring.
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Affiliation(s)
| | - Lucía Páiz‐Medina
- Molecular Biology CenterUniversity of Central America, UCAManaguaNicaragua
| | | | - Nelvia Hernández
- Institute of Interdisciplinary Research in Natural SciencesUniversity of Central America, UCAManaguaNicaragua
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Comparative mitochondrial genomes of the Rhus gall aphid Kaburagia rhusicola subspecies with variable gall shapes. Gene X 2022; 824:146379. [PMID: 35276238 DOI: 10.1016/j.gene.2022.146379] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Revised: 02/06/2022] [Accepted: 02/24/2022] [Indexed: 11/23/2022] Open
Abstract
Rhus gall aphids (Hemiptera: Aphididae: Eriosomatinae) stimulate the formation of galls on their primary host plants (sumacs: Rhus spp., Anacardiaceae). The shapes of galls are often used as an extended phenotype to identify the aphid species and subspecies. We collected four Rhus galls with conspicuously different shapes formed by Kaburagia rhusicola aphids, whose sequences of the complete mitochondrial genomes (mitogenomes) were obtained by high-throughput sequencing. Each mitogenome was assembled into a circular molecule containing 13 protein-coding genes, two rRNAs, 22 tRNAs and one control region. All the protein-coding genes had a typical ATN initiation codon and TAA termination codon except for cox1 and nad4, which had a single T as stop codon. All the tRNAs could be folded as a typical clover-leaf secondary structure, except for trnS1 lacking a dihydrouridine (DHU) arm. The relative synonymous codon usage and ratio of nonsynonymous to synonymous substitution rates showed that the four K. rhusicola samples were highly similar to the subspecies K. r. ovogallis. The phylogenetic analyses grouped these samples with K. r. ovogallis in a clade sister to K. r. rhusicola. All these molecular analyses demonstrated that our current samples represented one subspecies of Kaburagia rhusicola, i.e., K. r. ovogallis, and the gall shape was variable even at the subspecies level in Kaburagia gall aphids.
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Takagui FH, Baumgärtner L, Viana P, Lima MCC, Bitencourt JDA, Venere PC, Lui RL, Moreira-Filho O, Feldberg E, Almeida Simões F, Birindelli JL, Giuliano-Caetano L. Karyotype Evolution of Talking Thorny Catfishes Anadoras (Doradidae, Astrodoradinae): A Process Mediated by Structural Rearrangements and Intense Reorganization of Repetitive DNAs. Cytogenet Genome Res 2022; 162:64-75. [PMID: 35500552 DOI: 10.1159/000523747] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Accepted: 02/17/2022] [Indexed: 11/19/2022] Open
Abstract
Anadoras is a thorny catfish genus widespread through the Amazon and Paraguay river basins. It includes 2 nominal species, A. grypus and A. weddellii, plus Anadoras sp. "araguaia," an undescribed species only recognized morphologically. Since Anadoras occupies a basal position within the Astrodoradinae phylogeny, it is crucial to identify its cytogenetic features to comprehend the mechanisms involved in the chromosomal diversification of this subfamily. Therefore, we performed a comparative cytogenetic analysis including all species of Anadoras. Furthermore, we applied a species delimitation analysis based on 600 bp of the mitochondrial cytochrome oxidase subunit 1 (CO1) gene to investigate the taxonomic status of the species. Cytogenetic markers revealed a high degree of similarity among Anadoras weddellii and Anadoras sp. "araguaia," both have 2n = 56 chromosomes (24m + 10sm + 22st/a), single NOR sites on acrocentric pair 28, and 5S rDNA sites on submetacentric pair 15. A. grypus has the most divergent chromosomal characteristics because, even though it also has 2n = 56 chromosomes, it exhibits several differences in the chromosome formula, heterochromatin distribution, and number/position of the rDNA sites. In sum, we believe that the chromosome diversification of Anadoras is due to 4 mechanisms: centric fusion, pericentric/paracentric inversions, nonreciprocal translocations, and activity of transposable elements. Additionally, our phylogenetic tree revealed well-supported clades and, by barcode species delimitation analysis, confirmed the existence of 3 molecular operational taxonomic units, including the putative new species Anadoras sp. "araguaia."
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Affiliation(s)
- Fábio Hiroshi Takagui
- Laboratory of Animal Cytogenetics, Department of General Biology, CCB, State University of Londrina, Londrina, Brazil
| | - Lucas Baumgärtner
- Cytogenetic Laboratory, Center of Biological and Health Sciences, State University of Western Paraná, Cascavel, Brazil
| | - Patrik Viana
- Laboratory of Animal Genetics, National Institute of Amazonian Research, Manaus, Brazil
| | - Moema C C Lima
- Laboratory of Genetics and Animal Ecology, Department of General Biology, CCB, State University of Londrina, Londrina, Brazil
| | - Jamille de A Bitencourt
- Cytogenetic Laboratory, Department of Biological Sciences, State University of Southwest of Bahia, Jequié, Brazil
| | - Paulo Cesar Venere
- Laboratory of Animal Cytogenetics and Genetics, Federal University of Mato Grosso, Cuiabá, Brazil
| | - Roberto Laridondo Lui
- Cytogenetic Laboratory, Center of Biological and Health Sciences, State University of Western Paraná, Cascavel, Brazil
| | - Orlando Moreira-Filho
- Laboratory of Molecular Biodiversity and Conservation, Department of Genetics and Evolution, Federal University of São Carlos, São Carlos, Brazil
| | - Eliana Feldberg
- Laboratory of Animal Genetics, National Institute of Amazonian Research, Manaus, Brazil
| | - Fernanda Almeida Simões
- Laboratory of Genetics and Animal Ecology, Department of General Biology, CCB, State University of Londrina, Londrina, Brazil
| | - José Luis Birindelli
- Museum of Zoology, Department of Animal and Plant Biology, CCB, Londrina State University, Londrina, Brazil
| | - Lucia Giuliano-Caetano
- Laboratory of Animal Cytogenetics, Department of General Biology, CCB, State University of Londrina, Londrina, 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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13
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Iorgu IŞ, Iorgu EI, Stalling T, Puskás G, Chobanov D, Szövényi G, Moscaliuc LA, Motoc R, Tăuşan I, Fusu L. Ant crickets and their secrets: Myrmecophilus acervorum is not always parthenogenetic (Insecta: Orthoptera: Myrmecophilidae). Zool J Linn Soc 2021. [DOI: 10.1093/zoolinnean/zlab084] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Abstract
Previously considered as a thelytokous parthenogenetic species, the widespread ant cricket Myrmecophilus acervorum actually turns out to have a mixed reproductive system: our recent surveys in the central part of its distribution area has revealed the presence of both sexes. Detailed morphological and morphometric descriptions of the previously unknown males are here provided. New data on species distribution in south-eastern Europe are presented, including the first records of M. balcanicus in Bulgaria and of M. nonveilleri in Bulgaria and Hungary. Phylogenetic and phylogeographic analyses have revealed several haplotypes of M. acervorum in Europe, with six of them forming a parthenogenetic clade in populations distributed west of the Carpathians. We tested our samples for bacterial infection by Wolbachia and, surprisingly, Wolbachia was identified only in populations with both sexes and no amplification was obtained from parthenogenetic populations. Phylogenetic analyses performed with sequences pertaining to five nominal species related to M. acervorum, yielded topological congruent trees with four well-supported groups: one group with M. acervorum samples, the second group with M. nonveilleri samples, the third group with M. fuscus and M. gallicus samples, and the fourth group with samples of M. balcanicus. We performed species delineation tests on our sequences, which delimited between four to seven putative species.
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Affiliation(s)
| | - Elena Iulia Iorgu
- ‘Grigore Antipa’ National Museum of Natural History, Bucharest, Romania
| | | | | | - Dragan Chobanov
- Institute of Biodiversity and Ecosystem Research, Bulgarian Academy of Sciences, Sofia, Bulgaria
| | - Gergely Szövényi
- Department of Systematic Zoology & Ecology, ‘Eötvös Loránd’ University, Budapest, Hungary
| | | | - Rozalia Motoc
- ‘Grigore Antipa’ National Museum of Natural History, Bucharest, Romania
| | - Ioan Tăuşan
- Department of Environmental Sciences and Physics, Lucian Blaga University of Sibiu, Faculty of Sciences, Sibiu, Romania
| | - Lucian Fusu
- Research Group in Invertebrate Diversity and Phylogenetics, Faculty of Biology, Al. I. Cuza University, Iaşi, Romania
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14
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Venturelli NB, Takagui FH, Pompeo LRS, Rodriguez MS, da Rosa R, Giuliano-Caetano L. Cytogenetic markers to understand chromosome diversification and conflicting taxonomic issues in Rineloricaria (Loricariidae: Loricariinae) from Rio Grande do Sul coastal drainages. Biologia (Bratisl) 2021. [DOI: 10.1007/s11756-021-00748-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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15
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Souza CS, Silva GSC, Ochoa LE, Roxo FF, Costa-Silva GJ, Foresti F, Melo BF, Oliveira C. Molecular and morphological diversity in species of Kronichthys (Teleostei, Loricariidae) from Atlantic coastal rivers of Brazil. JOURNAL OF FISH BIOLOGY 2021; 98:668-679. [PMID: 33128401 DOI: 10.1111/jfb.14607] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Revised: 10/23/2020] [Accepted: 10/29/2020] [Indexed: 06/11/2023]
Abstract
The Neotropical catfish genus Kronichthys contains three species distributed along coastal rivers of southern and southeastern Brazil. Although phylogenetic hypotheses are available, the molecular and morphological diversity and species boundaries within the genus remain unexplored. In this study, the authors generated mitochondrial data for 90 specimens combined with morphometric and meristic data to investigate species diversity, species boundaries and putative morphological signatures in Kronichthys. Phylogenetic and species delimitation results clearly show the presence of four genetic lineages, three within Kronichthys heylandi along the coast from Rio de Janeiro to southern São Paulo and a single lineage encompassing both the nominal species Kronichthys lacerta and Kronichthys subteres from the Ribeira de Iguape basin to Santa Catarina in southern Brazil. Nonetheless, morphological data show overlapped ranges in morphometrics and a definition of only two morphotypes, with clear phenotypic differences in the teeth number: K. heylandi differs from K. subteres + K. lacerta by the higher number of premaxillary teeth (30-52 vs. 19-28) and higher number of dentary teeth (28-54 vs. 17-28). Headwater captures and connections of paleodrainages because of sea-level fluctuations represent the two major biogeographic processes promoting species diversification and lineage dispersal of Kronichthys in the Atlantic coastal range of Brazil.
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Affiliation(s)
- Camila S Souza
- Departamento de Biologia Estrutural e Funcional, Instituto de Biociências, Universidade Estadual Paulista, Botucatu, Brazil
| | - Gabriel S C Silva
- Departamento de Bioestatística, Biologia Vegetal, Parasitologia e Zoologia, Instituto de Biociências, Universidade Estadual Paulista, Botucatu, Brazil
| | - Luz E Ochoa
- Museu de Zoologia, Universidade de São Paulo, São Paulo, Brazil
| | - Fabio F Roxo
- Departamento de Bioestatística, Biologia Vegetal, Parasitologia e Zoologia, Instituto de Biociências, Universidade Estadual Paulista, Botucatu, Brazil
| | | | - Fausto Foresti
- Departamento de Biologia Estrutural e Funcional, Instituto de Biociências, Universidade Estadual Paulista, Botucatu, Brazil
| | - Bruno F Melo
- Departamento de Biologia Estrutural e Funcional, Instituto de Biociências, Universidade Estadual Paulista, Botucatu, Brazil
| | - Claudio Oliveira
- Departamento de Biologia Estrutural e Funcional, Instituto de Biociências, Universidade Estadual Paulista, Botucatu, Brazil
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16
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Fernandes CA, Paiz LM, Piscor D, Gavazzoni M, Carvalho LABD, Portela-Castro ALDB, Margarido VP. Chromosomal Diversity in Two Allopatric Populations of Farlowella hahni Meinken 1937 (Teleostei: Siluriformes): Cytogenetics and Cytochrome b Analyses. Zebrafish 2021; 18:66-72. [PMID: 33538653 DOI: 10.1089/zeb.2020.1966] [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: 11/13/2022] Open
Abstract
Farlowella is the second richest genus in Loricariinae, broadly distributed in freshwater streams and rivers of South America. In this article, we aimed to expand on the cytogenetic and molecular data available for two allopatric populations of Farlowella hahni. Both populations had diploid chromosome number 58, but with karyotype differences, indicative of chromosomal rearrangements. C-banding showed large heterochromatic blocks at telomeric regions in acrocentric chromosomes in both populations. Fluorescence in situ hybridization (FISH) revealed a single 18S rDNA site in both populations and a single 5S rDNA site for individuals from lower Paraná River basin (native region) and multiple 5S rDNA sites for individuals from upper Paraná River basin (non-native region). Mitochondrial sequence analyses did not separate the two F. hahni populations. The cytogenetic and molecular data obtained are relevant in a preliminary study and suggested the existence of cryptic diversity and the hypothesis that at least two Farlowella lineages may coexist in the Paraná basin.
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Affiliation(s)
- Carlos Alexandre Fernandes
- Departamento de Biotecnologia, Genética e Biologia Celular, Universidade Estadual de Maringá, Maringá, Brazil.,Programa de Pós-Graduação em Biologia Comparada, Universidade Estadual de Maringá, Maringá, Brazil
| | - Leonardo Marcel Paiz
- Programa de Pós-Graduação em Biologia Comparada, Universidade Estadual de Maringá, Maringá, Brazil.,Centro de Ciências Biológicas e da Saúde, Universidade Estadual do Oeste do Paraná, Cascavel, Brazil
| | - Diovani Piscor
- Universidade Estadual de Mato Grosso do Sul, Unidade Universitária de Mundo Novo, Dourados, Brazil
| | - Mariane Gavazzoni
- Programa de Pós-Graduação em Biologia Comparada, Universidade Estadual de Maringá, Maringá, Brazil.,Centro de Ciências Biológicas e da Saúde, Universidade Estadual do Oeste do Paraná, Cascavel, Brazil
| | | | | | - Vladimir Pavan Margarido
- Programa de Pós-Graduação em Biologia Comparada, Universidade Estadual de Maringá, Maringá, Brazil.,Centro de Ciências Biológicas e da Saúde, Universidade Estadual do Oeste do Paraná, Cascavel, Brazil
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17
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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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18
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Wattier R, Mamos T, Copilaş-Ciocianu D, Jelić M, Ollivier A, Chaumot A, Danger M, Felten V, Piscart C, Žganec K, Rewicz T, Wysocka A, Rigaud T, Grabowski M. Continental-scale patterns of hyper-cryptic diversity within the freshwater model taxon Gammarus fossarum (Crustacea, Amphipoda). Sci Rep 2020; 10:16536. [PMID: 33024224 PMCID: PMC7538970 DOI: 10.1038/s41598-020-73739-0] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Accepted: 09/16/2020] [Indexed: 12/11/2022] Open
Abstract
Traditional morphological diagnoses of taxonomic status remain widely used while an increasing number of studies show that one morphospecies might hide cryptic diversity, i.e. lineages with unexpectedly high molecular divergence. This hidden diversity can reach even tens of lineages, i.e. hyper cryptic diversity. Even well-studied model-organisms may exhibit overlooked cryptic diversity. Such is the case of the freshwater crustacean amphipod model taxon Gammarus fossarum. It is extensively used in both applied and basic types of research, including biodiversity assessments, ecotoxicology and evolutionary ecology. Based on COI barcodes of 4926 individuals from 498 sampling sites in 19 European countries, the present paper shows (1) hyper cryptic diversity, ranging from 84 to 152 Molecular Operational Taxonomic Units, (2) ancient diversification starting already 26 Mya in the Oligocene, and (3) high level of lineage syntopy. Even if hyper cryptic diversity was already documented in G. fossarum, the present study increases its extent fourfold, providing a first continental-scale insight into its geographical distribution and establishes several diversification hotspots, notably south-eastern and central Europe. The challenges of recording hyper cryptic diversity in the future are also discussed.
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Affiliation(s)
- Remi Wattier
- UMR CNRS 6282 Biogéosciences, Université Bourgogne Franche Comté, Dijon, France.
| | - Tomasz Mamos
- Department of Invertebrate Zoology and Hydrobiology, University of Lodz, Lodz, Poland.,Zoological Institute, University of Basel, Basel, Switzerland
| | - Denis Copilaş-Ciocianu
- Institute of Ecology, Nature Research Centre, Vilnius Nature Research Centre, Institute of Ecology, Vilnius, Lithuania
| | - Mišel Jelić
- Department of Natural Sciences, Varaždin City Museum, Varaždin, Croatia
| | - Anthony Ollivier
- UMR CNRS 6282 Biogéosciences, Université Bourgogne Franche Comté, Dijon, France
| | - Arnaud Chaumot
- Laboratoire d'écotoxicologie, INRAE, UR RiverLy, Villeurbanne, France
| | - Michael Danger
- UMR CNRS 73602 LIEC, Université de Lorraine, Metz, France
| | - Vincent Felten
- UMR CNRS 73602 LIEC, Université de Lorraine, Metz, France
| | | | - Krešimir Žganec
- Department of Teacher Education Studies in Gospić, University of Zadar, Gospić, Croatia
| | - Tomasz Rewicz
- Department of Invertebrate Zoology and Hydrobiology, University of Lodz, Lodz, Poland.,University of Guelph, Centre for Biodiversity Genomics, Guelph, ON, Canada
| | - Anna Wysocka
- Department of Genetics and Biosystematics, University of Gdansk, Gdansk, Poland
| | - Thierry Rigaud
- UMR CNRS 6282 Biogéosciences, Université Bourgogne Franche Comté, Dijon, France
| | - Michał Grabowski
- Department of Invertebrate Zoology and Hydrobiology, University of Lodz, Lodz, Poland.
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19
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Ceruso M, Mascolo C, De Luca P, Venuti I, Smaldone G, Biffali E, Anastasio A, Pepe T, Sordino P. A Rapid Method for the Identification of Fresh and Processed Pagellus erythrinus Species against Frauds. Foods 2020; 9:E1397. [PMID: 33023115 PMCID: PMC7600753 DOI: 10.3390/foods9101397] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Revised: 09/28/2020] [Accepted: 09/30/2020] [Indexed: 11/16/2022] Open
Abstract
The commercialization of porgies or seabreams of the family Sparidae has greatly increased in the last decade, and some valuable species have become subject to seafood substitution. DNA regions currently used for fish species identification in fresh and processed products belong to the mitochondrial (mt) genes cytochrome b (Cytb), cytochrome c oxidase I (COI), 16S and 12S. However, these markers amplify for fragments with lower divergence within and between some species, failing to provide informative barcodes. We adopted comparative mitogenomics, through the analysis of complete mtDNA sequences, as a compatible approach toward studying new barcoding markers. The intent is to develop a specific and rapid assay for the identification of the common pandora Pagellus erythrinus, a sparid species frequently subject to fraudulent replacement. The genetic diversity analysis (Hamming distance, p-genetic distance, gene-by-gene sequence variability) between 16 sparid mtDNA genomes highlighted the discriminating potential of a 291 bp NAD2 gene fragment. A pair of species-specific primers were successfully designed and tested by end-point and real-time PCR, achieving amplification only in P. erythrinus among several fish species. The use of the NAD2 barcoding marker provides a rapid presence/absence method for the identification of P. erythrinus.
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Affiliation(s)
- Marina Ceruso
- Department of Veterinary Medicine and Animal Production, University of Naples Federico II, via F. Delpino, n.1, 80137 Naples, Italy; (M.C.); (C.M.); (I.V.); (A.A.)
| | - Celestina Mascolo
- Department of Veterinary Medicine and Animal Production, University of Naples Federico II, via F. Delpino, n.1, 80137 Naples, Italy; (M.C.); (C.M.); (I.V.); (A.A.)
- Department of Biology and Evolution of Marine Organisms, Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Naples, Italy;
| | - Pasquale De Luca
- Department of Research Infrastructures for Marine Biological Resources, Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Naples, Italy; (P.D.L.); (E.B.)
| | - Iolanda Venuti
- Department of Veterinary Medicine and Animal Production, University of Naples Federico II, via F. Delpino, n.1, 80137 Naples, Italy; (M.C.); (C.M.); (I.V.); (A.A.)
| | - Giorgio Smaldone
- Department Agricultural Sciences, University of Naples Federico II, via Università, n.100, Portici, 80055 Naples, Italy;
| | - Elio Biffali
- Department of Research Infrastructures for Marine Biological Resources, Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Naples, Italy; (P.D.L.); (E.B.)
| | - Aniello Anastasio
- Department of Veterinary Medicine and Animal Production, University of Naples Federico II, via F. Delpino, n.1, 80137 Naples, Italy; (M.C.); (C.M.); (I.V.); (A.A.)
| | - Tiziana Pepe
- Department of Veterinary Medicine and Animal Production, University of Naples Federico II, via F. Delpino, n.1, 80137 Naples, Italy; (M.C.); (C.M.); (I.V.); (A.A.)
| | - Paolo Sordino
- Department of Biology and Evolution of Marine Organisms, Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Naples, Italy;
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20
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Takagui FH, Baumgärtner L, Venturelli NB, Paiz LM, Viana P, Dionísio JF, Pompeo LRS, Margarido VP, Fenocchio AS, da Rosa R, Giuliano-Caetano L. Unrevealing the Karyotypic Evolution and Cytotaxonomy of Armored Catfishes (Loricariinae) with Emphasis in Sturisoma, Loricariichthys, Loricaria, Proloricaria, Pyxiloricaria, and Rineloricaria. Zebrafish 2020; 17:319-332. [PMID: 32985966 DOI: 10.1089/zeb.2020.1893] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
This study provides new insight into the chromosomal diversification in Loricariinae. We analyzed nine species from different Brazilian hydrographic basins, using conventional and molecular cytogenetic methods, aiming to understand the karyotypic diversification, and contribute with cytotaxonomic markers in this group considered one of the most diverse of Loricariidae. Our results evidenced a high karyotypic variability in diploid number (2n) ranging from 2n = 54 (Loricariichthys platymetopon and Loricariichthys anus), 2n = 60 (Rineloricaria reisi and Rineloricaria parva), 2n = 62 (Proloricaria prolixa), 2n = 64 (Loricaria cataphracta complex species), 2n = 66 (Sturisoma barbatum), and 2n = 68 (Pyxiloricaria menezesi). Different patterns of 18S and 5S ribosomal DNA (rDNA) were also identified, while slight divergences in heterochromatin distribution were observed. This high variability is probably related with independent events of Robertsonian translocations, pericentric inversions, and different mechanisms of rDNA sites dispersion (nonreciprocal translocation and transposable element [TEs] co-localization). In addition, our study provides a set of efficient chromosomal markers for the characterization of all analyzed species, and certainly, in future analyzes, will contribute as a useful cytotaxonomic tool in groups where the traditional taxonomy based on morphological data are not sufficient to clarify their relationship.
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Affiliation(s)
- Fábio Hiroshi Takagui
- Animal Cytogenetics Laboratory, Department of General Biology, CCB, Londrina State University, Londrina, Brazil
| | - Lucas Baumgärtner
- Cytogenetic Laboratory, Center for Biological and Health Sciences, Western Paraná State University, Cascavel, Brazil
| | | | - Leonardo Marcel Paiz
- Cytogenetic Laboratory, Center for Biological and Health Sciences, Western Paraná State University, Cascavel, Brazil
| | - Patrik Viana
- Laboratory of Animal Genetics, National Institute of Amazonian Research, Manaus, Brazil
| | - Jaqueline Fernanda Dionísio
- Animal Cytogenetics Laboratory, Department of General Biology, CCB, Londrina State University, Londrina, Brazil
| | - Luis Ricardo Santana Pompeo
- Animal Cytogenetics Laboratory, Department of General Biology, CCB, Londrina State University, Londrina, Brazil
| | - Vladimir Pavan Margarido
- Cytogenetic Laboratory, Center for Biological and Health Sciences, Western Paraná State University, Cascavel, Brazil
| | | | - Renata da Rosa
- Animal Cytogenetics Laboratory, Department of General Biology, CCB, Londrina State University, Londrina, Brazil
| | - Lucia Giuliano-Caetano
- Animal Cytogenetics Laboratory, Department of General Biology, CCB, Londrina State University, Londrina, Brazil
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21
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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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22
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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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23
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Chagas ATDA, Ludwig S, Pimentel JDSM, de Abreu NL, Nunez-Rodriguez DL, Leal HG, Kalapothakis E. Use of complete mitochondrial genome sequences to identify barcoding markers for groups with low genetic distance. Mitochondrial DNA A DNA Mapp Seq Anal 2020; 31:139-146. [PMID: 32314625 DOI: 10.1080/24701394.2020.1748609] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
Complete mitochondrial sequences can be rapidly obtained and are widely available, providing a great source of species information and allowing for the discovery of new specific molecular markers. However, for some taxonomic groups, traditional approaches for species delimitation are impaired by the low genetic distance values. In these cases, other species-level markers are used. For Prochilodus, which includes important neotropical fish species, species-level delimitation usually results in poor phylogenetic resolution when using mitochondrial COI/cytB genes as barcoding markers because of low genetic variability and low species-level resolution. Thus, in this study, we developed an approach to design and validate new barcoding markers with high species-level resolution obtained from the D-loop region, using Prochilodus spp. as a model. For the new barcoding marker validation, the amplicon region was used to infer the phylogenetic relationships of Prochilodus spp. through three distinct methods: Bayesian inference (BI), Neighbor-Joining method (NJ), and Maximum Likelihood method (ML). The phylogenetic relationships of Prochilodus spp. revealed high resolution at species-level, nonoverlapping clades, and high branch support. The genetic distance results allied to two different clustering methods (Bayesian Poisson tree processes and automatic barcode gap discovery) revealed the existence of a barcoding gap, thus, validating the use of the barcoding markers designed in this study. The approach proposed here may, therefore, be expanded to other taxa to access and validate new barcoding markers with higher resolution at the species level.
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Affiliation(s)
- Aline Torres de Azevedo Chagas
- Department of Genetics, Ecology and Evolution, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, Brazil
| | - Sandra Ludwig
- Department of Genetics, Ecology and Evolution, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, Brazil
| | - Juliana da Silva Martins Pimentel
- Department of Genetics, Ecology and Evolution, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, Brazil.,Pitágoras College, Belo Horizonte, Brazil
| | - Nazaré Lúcio de Abreu
- Department of Genetics, Ecology and Evolution, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, Brazil
| | - Daniela Lidia Nunez-Rodriguez
- Department of Genetics, Ecology and Evolution, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, Brazil
| | - Hortensia Gomes Leal
- Department of Genetics, Ecology and Evolution, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, Brazil
| | - Evanguedes Kalapothakis
- Department of Genetics, Ecology and Evolution, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, Brazil
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Donin LM, Ferrer J, Carvalho TP. Taxonomical study of Trichomycterus (Siluriformes: Trichomycteridae) from the Ribeira de Iguape River basin reveals a new species recorded in the early 20th century. JOURNAL OF FISH BIOLOGY 2020; 96:886-904. [PMID: 32039475 DOI: 10.1111/jfb.14278] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2019] [Revised: 01/31/2020] [Accepted: 02/07/2020] [Indexed: 06/10/2023]
Abstract
A new species of Trichomycterus endemic to the Ribeira de Iguape River basin, southeastern Brazil, was studied based on morphological and molecular evidence. This species had an outer layer of coloration composed of scattered, round, black or dark-brown spots smaller or equivalent in size to the circumference of the eye; eight pectoral-fin rays; 28-29 opercular odontodes; 54-56 interopercular odontodes; and supraorbital line of the laterosensory system not interrupted, with pores s2 absent. Two other species of Trichomycterus from the Ribeira de Iguape River basin are recorded, and their taxonomic status is discussed: Trichomycterus alternatus and Trichomycterus jacupiranga were not differentiated using molecular analysis but may be consistently distinguished based on morphology. The phylogenetic relationships of the co-occurring species, T. alternatus and Cambeva zonata, were inferred using mitochondrial data, reinforcing the taxonomic status of these recently revised species that have a complex taxonomy. In addition, a new combination for Trichomycterus taroba with its inclusion in the genus Cambeva is recommended.
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Affiliation(s)
- Laura M Donin
- Departamento de Zoologia, Universidade Federal do Rio Grande do Sul, Programa de Pós-Graduação em Biologia Animal, Porto Alegre, Brazil
- Museu de Zoologia da Universidade de São Paulo, São Paulo, Brazil
| | - Juliano Ferrer
- Departamento de Zoologia, Universidade Federal do Rio Grande do Sul, Programa de Pós-Graduação em Biologia Animal, Porto Alegre, Brazil
| | - Tiago P Carvalho
- Departamento de Zoologia, Universidade Federal do Rio Grande do Sul, Programa de Pós-Graduação em Biologia Animal, Porto Alegre, Brazil
- Laboratorio de Ictiología, Unidad de Ecología y Sistemática (UNESIS), Departamento de Biología, Facultad de Ciencias, Pontificia Universidad Javeriana, Carrera, Bogotá DC, Colombia
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25
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Gavazzoni M, Pavanelli CS, Graça WJ, Melo BF, Gubiani ÉA, Margarido VP. Detection of natural hybridization and delimitation of two closely related operational taxonomic units of the Astyanax fasciatus (Teleostei: Characidae) complex through integrative approaches. Biol J Linn Soc Lond 2020. [DOI: 10.1093/biolinnean/blz199] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Abstract
Astyanax is a species-rich, non-monophyletic genus composed of several supraspecific taxa that are poorly delimited. The Astyanax fasciatus complex is one of these taxa and shows high taxonomic complexity. To elucidate the evolutionary history of the A. fasciatus complex from southern South America, we conducted cytogenetic, molecular and morphological analyses in specimens from the Uruguay River basin. Cytogenetic characters demonstrated two closely related operational taxonomic units: Astyanax sp. 1 (8m+22sm+10st+6a), Astyanax sp. 2 (8m+24sm+10st+4a) and natural hybrids (8m+23sm+8st+5a). 5S ribosomal DNA sites were found in two pairs of m chromosomes and one pair of a chromosomes in Astyanax sp. 1, two pairs of a chromosomes and one pair of m chromosomes in Astyanax sp. 2, and three m chromosomes and three a chromosomes in hybrids. As51 sites were found in three chromosomes in Astyanax sp. 1 and in five chromosomes in Astyanax sp. 2 and hybrids. Mitochondrial sequence analyses did not separate the two units and hybrids. Morphological analyses revealed differences between Astyanax sp. 2 and hybrids. This secondary contact with gene flow between lineages that diverged long ago might slow or reverse the differentiation/speciation process. These results help us to understand the evolutionary history of this highly complex clade of Astyanax in southern South America.
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Affiliation(s)
- Mariane Gavazzoni
- Universidade Estadual do Oeste do Paraná, Centro de Ciências Biológicas e da Saúde, Cascavel, Paraná, Brazil
- Universidade Estadual de Maringá, Pós-Graduação em Biologia Comparada, Maringá, Paraná, Brazil
| | - Carla S Pavanelli
- Universidade Estadual de Maringá, Pós-Graduação em Biologia Comparada, Maringá, Paraná, Brazil
- Universidade Estadual de Maringá, Núcleo de Pesquisas em Limnologia, Ictiologia e Aquicultura (NUPELIA), Maringá, Paraná, Brazil
| | - Weferson J Graça
- Universidade Estadual de Maringá, Pós-Graduação em Biologia Comparada, Maringá, Paraná, Brazil
- Universidade Estadual de Maringá, Núcleo de Pesquisas em Limnologia, Ictiologia e Aquicultura (NUPELIA), Maringá, Paraná, Brazil
- Universidade Estadual de Maringá, Departamento de Biologia, Maringá, Paraná, Brazil
| | - Bruno F Melo
- Universidade Estadual Paulista, Instituto de Biociências, Departamento de Morfologia, Laboratório de Biologia e Genética de Peixes, Botucatu, São Paulo, Brazil
| | - Éder André Gubiani
- Universidade Estadual do Oeste do Paraná, Grupo de Pesquisas em Recursos Pesqueiros e Limnologia (GERPEL), Pós Graduação em Recursos Pesqueiros e Engenharia de Pesca, Pós Graduação em Conservação e Manejo de Recursos Naturais, Toledo, Paraná, Brazil
| | - Vladimir P Margarido
- Universidade Estadual do Oeste do Paraná, Centro de Ciências Biológicas e da Saúde, Cascavel, Paraná, Brazil
- Universidade Estadual de Maringá, Pós-Graduação em Biologia Comparada, Maringá, Paraná, Brazil
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26
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Hashimoto S, Py-Daniel LHR, Batista JS. A molecular assessment of species diversity in Tympanopleura and Ageneiosus catfishes (Auchenipteridae: Siluriformes). JOURNAL OF FISH BIOLOGY 2020; 96:14-22. [PMID: 31631341 DOI: 10.1111/jfb.14173] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2019] [Accepted: 10/18/2019] [Indexed: 06/10/2023]
Abstract
In order to test the congruence of genetic data to the morphologically defined Neotropical catfish genera Tympanopleura and Ageneiosus and explore species diversity, we generated 17 DNA barcodes from five of six species of Tympanopleura and 12 of 13 species of Ageneiosus. To discriminate limits between species, an automatic barcode gap discovery (ABGD), a generalised mixed yule-coalescent model (GYMC) and fixed distance thresholds Kimura two-parameter (K2P; 3%) were used to discriminate putative species limits from the DNA barcodes. The ABGD, GMYC and K2P methods agreed by each generating 13 clusters: six in Tympanopleura (five nominal plus one undescribed species) and seven in Ageneiosus. These clusters corresponded broadly to the described species, except in the case of the Ageneiosus ucayalensis group (A. akamai, A. dentatus, A. intrusus, A. ucayalensis, A. uranophthalmus and A. vittatus). Haplotype sharing and low divergences may have prevented molecular methods from distinguishing these species. We hypothesise that this is the result of a recent radiation of a sympatric species group distributed throughout the Amazon Basin. One putative new species of Tympanopleura was also supported by the molecular data. These results taken together highlight the utility of molecular methods such as DNA barcoding in understanding patterns of diversification across large geographic areas and in recognising overlooked diversity.
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Affiliation(s)
- Shizuka Hashimoto
- Instituto Nacional de Pesquisas da Amazônia, Programa de Pós-Graduação em Genética, Conservação e Biologia Evolutiva, Manaus, Amazonas, Brazil
- Instituto Nacional de Pesquisas da Amazônia, Coleção de Peixes, Programa de Coleções Científicas, Manaus, Amazonas, Brazil
| | - Lúcia H Rapp Py-Daniel
- Instituto Nacional de Pesquisas da Amazônia, Coleção de Peixes, Programa de Coleções Científicas, Manaus, Amazonas, Brazil
| | - Jacqueline S Batista
- Instituto Nacional de Pesquisas da Amazônia, Laboratório Temático de Biologia Molecular, Manaus, Amazonas, Brazil
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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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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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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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Molecular Data Reveal Multiple Lineages in Piranhas of the Genus Pygocentrus (Teleostei, Characiformes). Genes (Basel) 2019; 10:genes10050371. [PMID: 31096658 PMCID: PMC6562675 DOI: 10.3390/genes10050371] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2019] [Revised: 05/09/2019] [Accepted: 05/13/2019] [Indexed: 11/26/2022] Open
Abstract
Carnivorous piranhas are distributed in four serrasalmid genera including Pygocentrus, which inhabit major river basins of South America. While P. cariba and P. piraya are endemics of the Orinoco and São Francisco basins, respectively, P. nattereri is widely distributed across the Amazonas, Essequibo, lower Paraná, Paraguay, and coastal rivers of northeastern Brazil, with recent records of introductions in Asia. Few studies have focused on the genetic diversity and systematics of Pygocentrus and the putative presence of additional species within P. nattereri has never been the subject of a detailed molecular study. Here we aimed to delimit species of Pygocentrus, test the phylogeographic structure of P. nattereri, and access the origin of introduced specimens of P. nattereri in Asia. Phylogenetic analyses based on a mitochondrial dataset involving maximum-likelihood tree reconstruction, genetic distances, Bayesian analysis, three delimitation approaches, and haplotype analysis corroborate the morphological hypothesis of the occurrence of three species of Pygocentrus. However, we provide here strong evidence that P. nattereri contains at least five phylogeographically-structured lineages in the Amazonas, Guaporé (type locality), Itapecuru, Paraná/Paraguay, and Tocantins/Araguaia river basins. We finally found that the introduced specimens in Asia consistently descend from the lineage of P. nattereri from the main Rio Amazonas. These results contribute to future research aimed to detect morphological variation that may occur in those genetic lineages of Pygocentrus.
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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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32
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Perdices A, Ozeren CS, Erkakan F, Freyhof J. Diversity of spined loaches from Asia Minor in a phylogenetic context (Teleostei: Cobitidae). PLoS One 2018; 13:e0205678. [PMID: 30308027 PMCID: PMC6181420 DOI: 10.1371/journal.pone.0205678] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2018] [Accepted: 09/29/2018] [Indexed: 11/19/2022] Open
Abstract
Accurate determination of species diversity in areas of high endemicity, particularly those lacking comprehensive systematic knowledge, represents a challenge for both taxonomists and conservationists. This need is particularly evident in areas greatly affected by anthropogenic disturbances such as the Eastern Mediterranean and its freshwater environments. To improve our knowledge of Eastern Mediterranean freshwater fishes, we phylogenetically studied Western Palearctic Cobitis species, focusing on those found in Turkey. Overall, our results provide a robust framework to assess the number of species of Cobitis. Phylogenetic reconstructions based on mitochondrial (cyt b) and nuclear (RAG1) sequences show seven major clades (Clades 1-7) grouping all Western Palearctic Cobitis species, except C. melanoleuca. In general, each major clade comprises Cobitis species that inhabit geographically close areas and have similar secondary sexual characters. Multiple divergent lineages were identified in our analyses, some of which were highly divergent such as the ones inhabiting Turkish freshwaters. Moreover, in some analyses, several of the identified lineages were incongruent with a priori defined species. Furthermore, our analyses identified eight potentially new candidate species, six that had been suggested in previous studies and two that are reported here for the first time. Our results reveal Turkey as the area with the greatest diversity of spined loaches in the Mediterranean.
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Affiliation(s)
- Anabel Perdices
- Department of Biodiversity and Evolutionary Biology, Museo Nacional de Ciencias Naturales, CSIC, Madrid, Spain
- * E-mail:
| | - Cevher S. Ozeren
- Department of Biology, Faculty of Science, University of Ankara, Ankara, Turkey
| | - Füsun Erkakan
- Department of Biology, Faculty of Science, Hacettepe University, Beytepe Campus, Ankara, Turkey
| | - Jörg Freyhof
- Leibniz-Institute of Freshwater Ecology and Inland Fisheries (IGB), Berlin, Germany
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33
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Cardoso YP, Rosso JJ, Mabragaña E, González-Castro M, Delpiani M, Avigliano E, Bogan S, Covain R, Schenone NF, Díaz de Astarloa JM. A continental-wide molecular approach unraveling mtDNA diversity and geographic distribution of the Neotropical genus Hoplias. PLoS One 2018; 13:e0202024. [PMID: 30102742 PMCID: PMC6089427 DOI: 10.1371/journal.pone.0202024] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2018] [Accepted: 07/26/2018] [Indexed: 01/26/2023] Open
Abstract
With an estimate of around 9,000 species, the Neotropical region hosts the greatest diversity of freshwater fishes of the world. Genetic surveys have the potential to unravel isolated and unique lineages and may result in the identification of undescribed species, accelerating the cataloguing of extant biodiversity. In this paper, molecular diversity within the valuable and widespread Neotropical genus Hoplias was assessed by means of DNA Barcoding. The geographic coverage spanned 40 degrees of latitude from French Guiana to Argentina. Our analyses revealed 22 mitochondrial lineages fully supported by means of Barcode Index Number, Automatic Barcode Gap Discovery and phylogenetic analyses. This mtDNA survey revealed the existence of 15 fully supported mitochondrial lineages within the once considered to be the continentally distributed H. malabaricus. Only four of them are currently described as valid species however, leaving 11 mitochondrial lineages currently "masked" within this species complex. Mean genetic divergence was 13.1%. Barcoding gap analysis discriminated 20 out of the 22 lineages tested. Phylogenetic analyses showed that all taxonomically recognized species form monophyletic groups. Hoplias malabaricus sensu stricto clustered within a large clade, excluding the representatives of the La Plata River Basin. In the H. lacerdae group, all species but H. curupira showed a cohesive match between taxonomic and molecular identification. Two different genetic lineages were recovered for H. aimara. Given the unexpected hidden mitochondrial diversity within H. malabaricus, the COI sequence composition of specimens from Suriname (the type locality), identified as H. malabaricus sensu stricto, is of major importance.
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Affiliation(s)
- Yamila P. Cardoso
- Laboratorio de Sistemática y Biología Evolutiva, Facultad de Ciencias Naturales y Museo, Universidad Nacional de La Plata, La Plata, Buenos Aires, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas, Buenos Aires, Argentina
| | - Juan J. Rosso
- Consejo Nacional de Investigaciones Científicas y Técnicas, Buenos Aires, Argentina
- Grupo de Biotaxonomía Morfológica y Molecular de Peces, Instituto de Investigaciones Marinas y Costeras, Universidad Nacional de Mar del Plata, Mar del Plata, Argentina
- Fundación Bosques Nativos Argentinos para la Biodiversidad, Buenos Aires, Argentina
| | - Ezequiel Mabragaña
- Consejo Nacional de Investigaciones Científicas y Técnicas, Buenos Aires, Argentina
- Grupo de Biotaxonomía Morfológica y Molecular de Peces, Instituto de Investigaciones Marinas y Costeras, Universidad Nacional de Mar del Plata, Mar del Plata, Argentina
- Fundación Bosques Nativos Argentinos para la Biodiversidad, Buenos Aires, Argentina
| | - Mariano González-Castro
- Consejo Nacional de Investigaciones Científicas y Técnicas, Buenos Aires, Argentina
- Grupo de Biotaxonomía Morfológica y Molecular de Peces, Instituto de Investigaciones Marinas y Costeras, Universidad Nacional de Mar del Plata, Mar del Plata, Argentina
| | - Matías Delpiani
- Consejo Nacional de Investigaciones Científicas y Técnicas, Buenos Aires, Argentina
- Grupo de Biotaxonomía Morfológica y Molecular de Peces, Instituto de Investigaciones Marinas y Costeras, Universidad Nacional de Mar del Plata, Mar del Plata, Argentina
| | - Esteban Avigliano
- Consejo Nacional de Investigaciones Científicas y Técnicas, Buenos Aires, Argentina
- Fundación Bosques Nativos Argentinos para la Biodiversidad, Buenos Aires, Argentina
- Instituto de Investigaciones en Producción Animal, Facultad de Ciencias Veterinarias, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Sergio Bogan
- Fundación de Historia Natural “Félix de Azara”, Departamento de Ciencias Naturales y Antropología, Universidad Maimónides, Buenos Aires, Argentina
| | - Raphael Covain
- Department of Herpetology and Ichthyology, Museum of Natural History, Geneva, Switzerland
| | - Nahuel F. Schenone
- Centro de Investigaciones Antonia Ramos, Villa Bonita, Campo Ramón, Misiones, Argentina
| | - Juan M. Díaz de Astarloa
- Consejo Nacional de Investigaciones Científicas y Técnicas, Buenos Aires, Argentina
- Grupo de Biotaxonomía Morfológica y Molecular de Peces, Instituto de Investigaciones Marinas y Costeras, Universidad Nacional de Mar del Plata, Mar del Plata, Argentina
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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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Müller MI, Morais DH, Costa-Silva GJ, Aguiar A, Ávila RW, da Silva RJ. Diversity in the genusRhabdias(Nematoda, Rhabdiasidae): Evidence for cryptic speciation. ZOOL SCR 2018. [DOI: 10.1111/zsc.12304] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Affiliation(s)
- Maria I. Müller
- Department of Parasitology, Rua Professor Doutor Antônio Celso Wagner Zanin; Institute of Biosciences, São Paulo State University (UNESP); Botucatu São Paulo Brazil
| | - Drausio H. Morais
- Universidade Federal Rural da Amazônia (UFRA); Parauapebas Pará Brazil
| | - Guilherme J. Costa-Silva
- Department of Morphology, Rua Professor Doutor Antônio Celso Wagner Zanin; Institute of Biosciences, São Paulo State University (UNESP); Botucatu São Paulo Brazil
- Universidade Santo Amaro, Rua Prof. Enéas de Siqueira Neto, Jardim das Imbuias; São Paulo Brazil
| | - Aline Aguiar
- Department of Parasitology, Rua Professor Doutor Antônio Celso Wagner Zanin; Institute of Biosciences, São Paulo State University (UNESP); Botucatu São Paulo Brazil
| | - Robson W. Ávila
- Departamento de Química Biológica, Laboratório de Herpetologia; Universidade Regional do Cariri (URCA); Crato Ceará Brazil
| | - Reinaldo J. da Silva
- Department of Parasitology, Rua Professor Doutor Antônio Celso Wagner Zanin; Institute of Biosciences, São Paulo State University (UNESP); Botucatu São Paulo Brazil
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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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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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Camelier P, Menezes NA, Costa-Silva GJ, Oliveira C. Molecular and morphological data of the freshwater fish Glandulocauda melanopleura (Characiformes: Characidae) provide evidences of river captures and local differentiation in the Brazilian Atlantic Forest. PLoS One 2018; 13:e0194247. [PMID: 29579069 PMCID: PMC5868800 DOI: 10.1371/journal.pone.0194247] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2017] [Accepted: 02/27/2018] [Indexed: 01/16/2023] Open
Abstract
The current distribution of freshwater fishes across multiple basins along Eastern Brazil can be associated to two main events: river captures or temporary paleoconnections. Apparently, river captures had a more significant role on distribution and structuring of species from upland areas, such as Glandulocauda melanopleura. Populations of this species are found in contiguous drainages in presently isolated upper parts of Rio Tietê and the coastal basins of Guaratuba, Itatinga, Itanháem, and Ribeira de Iguape, in the Atlantic Forest domain. The allopatric and disjoint distribution of G. melanopleura associated with variation of morphological characters detected among geographically isolated populations stimulated this study. Thus, an integrative approach was undertaken, including morphological and molecular data, to better understand the evolutionary history of the species and the area where it occurs. Molecular analyses based on two mitochondrial markers revealed a strong genetic structure within G. melanopleura, that allowed recognition of two lineages, one distributed in both the upper Tietê and Itanhaém and the other in the Guaratuba. Overall, morphological data revealed some intraspecific overlapping variation, indicating that all samples are conspecific. Phylogenetic and phylogeographic analyses allied to divergence times and geomorphological information indicate that the current distribution of G. melanopleura is a result of relatively recent river captures involving the Tietê and some other coastal drainages. Although of recent origin, they occurred long enough to completely isolate these populations, since there are no haplotypes sharing between them. The conservation status of this species is also discussed, and our results corroborate the need to understand population structure for conservation planning.
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Affiliation(s)
- Priscila Camelier
- Museu de Zoologia da Universidade de São Paulo, CEP, São Paulo, SP, Brazil
| | | | - Guilherme José Costa-Silva
- Universidade Santo Amaro, Rua Prof. Enéas de Siqueira Neto, Jardim das Imbuias, CEP, São Paulo, SP, Brazil
| | - Claudio Oliveira
- Laboratório de Biologia e Genética de Peixes, Departamento de Morfologia, Instituto de Biociências, Universidade Estadual Paulista, Distrito Rubião Jr., CEP, Botucatu, SP, 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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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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41
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Fisch-Muller S, Mol JHA, Covain R. An integrative framework to reevaluate the Neotropical catfish genus Guyanancistrus (Siluriformes: Loricariidae) with particular emphasis on the Guyanancistrus brevispinis complex. PLoS One 2018; 13:e0189789. [PMID: 29298344 PMCID: PMC5752014 DOI: 10.1371/journal.pone.0189789] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2017] [Accepted: 12/03/2017] [Indexed: 11/29/2022] Open
Abstract
Characterizing and naming species becomes more and more challenging due to the increasing difficulty of accurately delineating specific bounderies. In this context, integrative taxonomy aims to delimit taxonomic units by leveraging the complementarity of multiple data sources (geography, morphology, genetics, etc.). However, while the theoretical framework of integrative taxonomy has been explicitly stated, methods for the simultaneous analysis of multiple data sets are poorly developed and in many cases different information sources are still explored successively. Multi-table methods developed in the field of community ecology provide such an intregrative framework. In particular, multiple co-inertia analysis is flexible enough to allow the integration of morphological, distributional, and genetic data in the same analysis. We have applied this powerfull approach to delimit species boundaries in a group of poorly differentiated catfishes belonging to the genus Guyanancistrus from the Guianas region of northeastern South America. Because the species G. brevispinis has been claimed to be a species complex consisting of five species, particular attention was paid to taxon. Separate analyses indicated the presence of eight distinct species of Guyanancistrus, including five new species and one new genus. However, none of the preliminary analyses revealed different lineages within G. brevispinis, and the multi-table analysis revealed three intraspecific lineages. After taxonomic clarifications and description of the new genus, species and subspecies, a reappraisal of the biogeography of Guyanancistrus members was performed. This analysis revealed three distinct dispersals from the Upper reaches of Amazonian tributaries toward coastal rivers of the Eastern Guianas Ecoregion. The central role played by the Maroni River, as gateway from the Amazon basin, was confirmed. The Maroni River was also found to be a center of speciation for Guyanancistrus (with three species and two subspecies), as well as a source of dispersal of G. brevispinis toward the other main basins of the Eastern Guianas.
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Affiliation(s)
- Sonia Fisch-Muller
- Natural History Museum, Department of Herpetology and Ichthyology, Geneva, Switzerland
| | - Jan H. A. Mol
- Center for Agricultural Research in Suriname (CELOS) and Department of Biology, Anton de Kom University of Suriname, Paramaribo, Suriname
| | - Raphaël Covain
- Natural History Museum, Department of Herpetology and Ichthyology, Geneva, Switzerland
- * E-mail:
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Marceniuk AP, Siccha-Ramirez R, Barthem RB, Wosiacki WB. Redescription of Notarius grandicassis and Notarius parmocassis (Siluriformes; Ariidae), with insights into morphological plasticity and evidence of incipient speciation. SYST BIODIVERS 2017. [DOI: 10.1080/14772000.2016.1256916] [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]
Affiliation(s)
- Alexandre P. Marceniuk
- Museu Paraense Emílio Goeldi, 6604-170, Belém, PA, Brazil
- Acervo Zoológico, Universidade Santa Cecília, 11045-907, Santos, SP, Brazil
| | - Raquel Siccha-Ramirez
- Laboratorio de Biologia e Genética de Peixes, Instituto de Biociencias, UNESP, 18618-689, Botucatu, SP, Brazil
- Laboratorio Costero de Tumbes, Instituto del Mar del Peru, Tumbes, Perú
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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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A New Species of Tiger Pleco Panaqolus (Siluriformes: Loricariidae) from the Xingu Basin, Brazil. PLoS One 2016; 11:e0165388. [PMID: 27828981 PMCID: PMC5102395 DOI: 10.1371/journal.pone.0165388] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2016] [Accepted: 10/10/2016] [Indexed: 11/30/2022] Open
Abstract
Panaqolus tankei is described from the Xingu River, Brazil. The new species is diagnosed from P. albomaculatus, P. dentex, P. nix, P. nocturnus, and P. koko by its color pattern consisting of dark and light diagonal bars on the body and bands on the fins (vs. body and fins without bars or bands); from P. albivermis, P. maccus, and P. purusiensis by the width of the dark bars being more or less the same of the light bars (vs. dark bars at least two or three times wider than light bars) and from P. changae by the absence of vermiculation on the head (vs. vermiculation present on head). The new species differs from P. gnomus by the orientation of the bars from posterodorsal to anteroventral direction (vs. anterodorsal to posteroventral direction), and from P. claustellifer by the orientation of the bands in the dorsal fin that are not parallel to the margin (vs. parallel to the margin). The barcoding region (COI) was sequenced for the new species, sequences were deposited in GenBank and were compared with congeners from other drainages. With regard to the current construction of a hydroelectric power plant (a so-called mega dam) in the Xingu River, herewith we increase knowledge of the river Xingu’s ichthyofauna and, thus improve the assessment of the impacts of that construction on the river.
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Barreto SB, Nunes LA, da Silva AT, Jucá-Chagas R, Diniz D, Sampaio I, Schneider H, Affonso PRADM. Is Nematocharax (Actinopterygii, Characiformes) a monotypic fish genus? Genome 2016; 59:851-865. [PMID: 27608265 DOI: 10.1139/gen-2015-0166] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The combination of DNA barcodes and geometric morphometrics is useful to discriminate taxonomically controversial species, providing more precise estimates of biodiversity. Therefore, our goal was to assess the genetic and morphometric diversity in Nematocharax, a controversial monotypic and sexually dimorphic genus of Neotropical fish, based on sequencing of cytochrome c oxidase subunit I (COI) and morphometric analyses in seven populations of N. venustus from coastal rivers in Brazil. The average pairwise intrapopulation divergence in COI ranged from 0 to 2.2%, while the average pairwise interpopulation divergence varied from 0 to 7.5%. The neighbour-joining (NJ) tree resulted in five genetic groups (bootstrap ≥ 97%), which correspond to the five clusters delimited by the BIN System, GMYC, and bPTP, indicating that there might be at least five species (or OTUs) within Nematocharax. Morphometric differences among these genetic lineages were also identified. Apparently, sexual selection, restricted dispersal, and geographic isolation might have acted synergistically to cause the evolutionary split of populations. These data challenge the current view that Nematocharax is a monotypic genus inasmuch as evolutionarily significant units or even distinguished species were identified. Therefore, we recommend that the highly impacted coastal basins in northeastern Brazil should be prioritized in conservation plans.
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Affiliation(s)
- Silvia Britto Barreto
- a Department of Biological Sciences, Universidade Estadual do Sudoeste da Bahia, Av. José Moreira Sobrinho, s/n, Jequiezinho, 45206190, Jequié, Bahia, Brazil
| | - Lorena Andrade Nunes
- a Department of Biological Sciences, Universidade Estadual do Sudoeste da Bahia, Av. José Moreira Sobrinho, s/n, Jequiezinho, 45206190, Jequié, Bahia, Brazil
| | - André Teixeira da Silva
- b Department of Zoology, Biosciences Institute, Universidade Estadual Paulista Júlio de Mesquita Filho, Av. 24-A, 1515, Bela Vista, 13506970, Rio Claro, São Paulo, Brazil
| | - Ricardo Jucá-Chagas
- a Department of Biological Sciences, Universidade Estadual do Sudoeste da Bahia, Av. José Moreira Sobrinho, s/n, Jequiezinho, 45206190, Jequié, Bahia, Brazil
| | - Débora Diniz
- a Department of Biological Sciences, Universidade Estadual do Sudoeste da Bahia, Av. José Moreira Sobrinho, s/n, Jequiezinho, 45206190, Jequié, Bahia, Brazil
| | - Iracilda Sampaio
- c Coastal Studies Institute, Universidade Federal do Pará, Alameda Leandro Ribeiro, s/n, Aldeia, 68600000, Bragança, Pará, Brazil
| | - Horacio Schneider
- c Coastal Studies Institute, Universidade Federal do Pará, Alameda Leandro Ribeiro, s/n, Aldeia, 68600000, Bragança, Pará, Brazil
| | - Paulo Roberto Antunes de Mello Affonso
- a Department of Biological Sciences, Universidade Estadual do Sudoeste da Bahia, Av. José Moreira Sobrinho, s/n, Jequiezinho, 45206190, Jequié, Bahia, Brazil
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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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