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Escobar Camacho D, Barragán KS, Guayasamin JM, Gavilanes G, Encalada AC. New records of native and introduced fish species in a river basin of Western Ecuador, the Chocó-Darien Ecoregion, using DNA barcoding. PLoS One 2024; 19:e0298970. [PMID: 38457426 PMCID: PMC10923491 DOI: 10.1371/journal.pone.0298970] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Accepted: 02/01/2024] [Indexed: 03/10/2024] Open
Abstract
DNA barcoding, based on mitochondrial markers, is widely applied in species identification and biodiversity studies. The aim of this study was to establish a barcoding reference database of fishes inhabiting the Cube River from Western Ecuador in the Chocó-Darien Global Ecoregion (CGE), a threatened ecoregion with high diversity and endemism, and evaluate the applicability of using barcoding for the identification of fish species. Barcode sequences were obtained from seven orders, 17 families, 23 genera and 26 species, which were validated through phylogenetic analysis, morphological measurements, and literature review. Our results showed that 43% of fish species in this region are endemic, confirmed the presence of known species in the area, and included the addition of three new records of native (Hoplias microlepis, Rhamdia guatemalensis and Sicydium salvini) and an introduced species (Xiphophorus maculatus) to Ecuador. In addition, eight species were barcoded for the first time. Species identification based on barcoding and morphology showed discrepancy with species lists from previous studies in the CGE, suggesting that the current baseline of western fishes of Ecuador is still incomplete. Because this study analyzed fishes from a relatively small basin (165 km2), more molecular-based studies focusing on fish are needed to achieve a robust sequence reference library of species inhabiting Western Ecuador. The new sequences of this study will be useful for future comparisons and biodiversity monitoring, supporting the application of barcoding tools for studying fish diversity in genetically unexplored regions and to develop well-informed conservation programs.
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Affiliation(s)
- Daniel Escobar Camacho
- Laboratorio de Ecología Acuática, Instituto BIOSFERA, Universidad San Francisco de Quito, Quito, Ecuador
| | - Karla S. Barragán
- Laboratorio de Ecología Acuática, Instituto BIOSFERA, Universidad San Francisco de Quito, Quito, Ecuador
| | - Juan M. Guayasamin
- Laboratorio de Biología Evolutiva, Instituto BIOSFERA, Universidad San Francisco de Quito, Quito, Ecuador
| | - Gabriela Gavilanes
- Laboratorio de Biología Evolutiva, Instituto BIOSFERA, Universidad San Francisco de Quito, Quito, Ecuador
| | - Andrea C. Encalada
- Laboratorio de Ecología Acuática, Instituto BIOSFERA, Universidad San Francisco de Quito, Quito, Ecuador
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Bockmann FA, Ferrer J, Rizzato PP, Esguícero ALH, Duboc LF, Ingenito LFS. Anatomy, ecology, and behavior of a new species of Scleronema Eigenmann, 1917 (Siluriformes: Trichomycteridae) from coastal drainages in the southern Brazilian Atlantic Rainforest, with comments on the monophyly and phylogeny of the genus. Zootaxa 2023; 5297:1-47. [PMID: 37518811 DOI: 10.11646/zootaxa.5297.1.1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Indexed: 08/01/2023]
Abstract
A new species of Scleronema (Trichomycteridae) is described from the lowlands of three coastal river basins in the Atlantic Forest of the Santa Catarina state, Southern Brazil. Aspects of the anatomy, reproduction, diet, feeding behavior and habitat of the new species are described and discussed in comparison with related taxa. The conservation status of the new species, which currently faces several threats due to environmental impacts on its region of occurrence, is established. Based on characteristics observed in the new species, as well as in most of its congeners, the phylogenetic position and monophyly of Scleronema are discussed and traits considered synapomorphic for the subgenera Plesioscleronema and Scleronema are reviewed. The monophyly of the genus Scleronema is supported by a new synapomorphy. In addition, two new synapomorphies, one of which based on behavior, are suggested for the subgenus Scleronema, justifying the inclusion of the new species. Within the subgenus Scleronema, the new species is assigned to the S. minutum group, which currently includes the majority of species of the genus, due to the presence of synapomorphic traits related to the body shape, maxillary barbel, skin flap of the opercle, caudal and pectoral fins, as well as osteological features of the lower jaw, hyoid arch, and postcranial axial skeleton. The species herein described differs from all its congeners by a combination of characters from various morphological complexes, which are described in detail using different methodologies, including radiography, whole-specimen clearing and double-staining procedures, and tridimensional computer nanotomography (3D nano-CT).
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Affiliation(s)
- Flávio A Bockmann
- Laboratório de Ictiologia de Ribeirão Preto - LIRP; Departamento de Biologia; Faculdade de Filosofia; Ciências e Letras de Ribeirão Preto; Universidade de São Paulo; Av. dos Bandeirantes; 3900; 14040-901 Ribeirão Preto; SP; Brazil; Programa de Pós-graduação em Biologia Comparada; Faculdade de Filosofia; Ciências e Letras de Ribeirão Preto; Universidade de São Paulo; Av. dos Bandeirantes; 3900; 14040-901 Ribeirão Preto; SP; Brazil.
| | - Juliano Ferrer
- Laboratório de Ictiologia; Programa de Pós-Graduação em Biologia Animal; Departamento de Zoologia; Instituto de Biociências; Universidade Federal do Rio Grande do Sul; Av. Bento Gonçalves; 9500; 91501-970 Porto Alegre; RS; Brazil.
| | - Pedro P Rizzato
- Departamento de Zoologia; Instituto de Biociências; Universidade de São Paulo; Rua do Matão; travessa 14; no. 101; 05508-090 São Paulo; SP; Brazil.
| | - André L H Esguícero
- Laboratório de Ictiologia de Ribeirão Preto - LIRP; Departamento de Biologia; Faculdade de Filosofia; Ciências e Letras de Ribeirão Preto; Universidade de São Paulo; Av. dos Bandeirantes; 3900; 14040-901 Ribeirão Preto; SP; Brazil; Programa de Pós-graduação em Biologia Comparada; Faculdade de Filosofia; Ciências e Letras de Ribeirão Preto; Universidade de São Paulo; Av. dos Bandeirantes; 3900; 14040-901 Ribeirão Preto; SP; Brazil.
| | - Luiz F Duboc
- Departamento de Ciências Agrárias e Biológicas - DCAB; Centro Universitário Norte do Espírito Santo - CEUNES; Universidade Federal do Espírito Santo; Rodovia BR-101 Norte; km 60; 29932-540 São Mateus; ES; Brazil.
| | - Leonardo F S Ingenito
- Departamento de Ciências Agrárias e Biológicas - DCAB; Centro Universitário Norte do Espírito Santo - CEUNES; Universidade Federal do Espírito Santo; Rodovia BR-101 Norte; km 60; 29932-540 São Mateus; ES; Brazil.
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Becker LA, Battini MA, Barriga JP, Azpelicueta MM, Johnson JB, Cussac VE. Morphologic and genetic variation within a relict Andean catfish, Hatcheria macraei , and its relationship with Trichomycterus areolatus and Bullockia maldonadoi (Siluriformes: Trichomycteridae). AN ACAD BRAS CIENC 2023; 95:e20211007. [PMID: 37162081 DOI: 10.1590/0001-3765202320211007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Accepted: 04/15/2022] [Indexed: 05/11/2023] Open
Abstract
The South American siluriform fishes are found primarily in the Neotropical region, north and east of the Colorado River of Argentina, with a few relict species distributed southward and westward on both sides of the Andes Mountains. Three of these, the closely related trichomycterids Hatcheria macraei, Trichomycterus areolatus and Bullockia maldonadoi, have been subject to historical taxonomic and nomenclatural arrangements. Here, we amplify a 652-bp fragment of COI mtDNA from 55 H. macraei individuals and use publicly available Cytb mtDNA sequences of the three taxa to assess their relationship, genetic variation and haplotype distribution in relation to hydrographic basins. In addition, we extend a recent morphometric study on H. macraei by analyzing body shape in 447 individuals collected from 24 populations across their entire cis-Andean distribution. We identified some lineages previously assigned to T. areolatus that show a closer relationship to either B. maldonadoi or H. macraei, revealing new boundaries to their currently known trans-Andean distribution. We found a great morphologic variation among H. macraei populations and a high genetic variation in H. macraei, T. areolatus and B. maldonadoi associated with river basins. We highlight further integrative studies are needed to enhance our knowledge of the southern Andean trichomycterid diversity.
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Affiliation(s)
- Leandro A Becker
- CONICET, Instituto de Diversidad y Evolución Austral (IDEAus), 9120 Puerto Madryn, Chubut, Argentina
| | - Miguel A Battini
- Universidad Nacional del Comahue, CONICET, Instituto de Investigaciones en Biodiversidad y Medioambiente (INIBIOMA), 8400 Bariloche, Río Negro, Argentina
| | - Juan P Barriga
- Universidad Nacional del Comahue, CONICET, Instituto de Investigaciones en Biodiversidad y Medioambiente (INIBIOMA), 8400 Bariloche, Río Negro, Argentina
| | - María M Azpelicueta
- Universidad Nacional de La Plata, CONICET, Facultad de Ciencias Naturales y Museo, 1900 La Plata, Buenos Aires, Argentina
| | - Jerald B Johnson
- Bean Life Science Museum, Department of Biology and Monte L., Brigham Young University, Provo, UT 84602, USA
| | - Víctor E Cussac
- Universidad Nacional del Comahue, CONICET, Instituto Andino Patagónico de Tecnologías Biológicas y Geoambientales (IPATEC), 8400 Bariloche, Río Negro, Argentina
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Vilardo PJ, Katz AM, Costa WJEM. Phylogenetic position of Trichomycterus astromycterus (Siluriformes: Trichomycteridae), an enigmatic trichomycterid from eastern Brazil, inferred from molecular data. JOURNAL OF FISH BIOLOGY 2022; 100:1093-1096. [PMID: 35191025 DOI: 10.1111/jfb.15015] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Revised: 02/02/2022] [Accepted: 02/16/2022] [Indexed: 06/14/2023]
Abstract
Recently in this journal, a new trichomycterine from eastern Brazil, Trichomycterus astromycterus, was described and considered possibly related to the Chilean Bullockia maldonadoi due to morphological similarities. Subsequently, osteological data supported T. astromycterus in the subgenus Psammocambeva of Trichomycterus, from eastern Brazil. Phylogenetic analyses, performed here, using a multigene data set for a broad trichomycterine sample, corroborate T. astromycterus as a member of Psammocambeva, reinforcing the importance of molecular data for inferring trichomycterine relationships but showing that osteological data alone may infer correctly phylogenetic placements when using broad comparative databases.
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Affiliation(s)
- Paulo J Vilardo
- Laboratory of Systematics and Evolution of Teleost Fishes, Institute of Biology, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Axel M Katz
- Laboratory of Systematics and Evolution of Teleost Fishes, Institute of Biology, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Wilson J E M Costa
- Laboratory of Systematics and Evolution of Teleost Fishes, Institute of Biology, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
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Costa WJ, Sampaio WM, Giongo P, de Almeida FB, Azevedo-Santos VM, Katz AM. An enigmatic interstitial trichomycterine catfish from south-eastern Brazil found at about 1000 km away from its sister group (Siluriformes: Trichomycteridae). ZOOL ANZ 2022. [DOI: 10.1016/j.jcz.2022.02.007] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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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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Donin LM, Ferrer J, Carvalho TP. Uncertainties and risks in delimiting species of Cambeva (Siluriformes: Trichomycteridae) with single-locus methods and geographically restricted data. NEOTROPICAL ICHTHYOLOGY 2022. [DOI: 10.1590/1982-0224-2022-0019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Abstract Cambeva contains species with complex taxonomy or poorly delimitated in terms of morphology and geopraphic distribution. We conducted an extensive review of Cambeva populations from coastal drainages of Southern to Southeastern Brazil to evaluate species geographic limits with an integrative analysis including morphological and molecular data (COI). We test if two single-locus methods, Bayesian Poisson Tree Processes (bPTP) and Generalized Mixed Yule Coalescent (GMYC), are efficient to delimit species boundaries in Cambeva by the comparison with the diagnosable morphological units. Using GMYC, we also evaluated the combination of tree and molecular clock priors to reconstruct the input phylogeny and assessed how well the implemented model fitted our empirical data. Eleven species were identified using a morphological diagnosability criterion: Cambeva balios, C. barbosae, C. botuvera, C. cubataonis, C. davisi, C. guaraquessaba, C. iheringi, C. tupinamba, and C. zonata and two treated as undescribed species. In contrast with previous knowledge, many of them have wider distribution and high intraspecific variation. Species delimitation based on single-locus demonstrated incongruences between the methods and strongly differed from the morphological delimitation. These disagreements and the violation of the GMYC model suggest that a single-locus data is insufficient to delimit Cambeva species and the failure may be attributable to events of mitochondrial introgression and incomplete lineage sorting.
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Costa WJ, Mattos JLO, Katz AM. Two new catfish species from central Brazil comprising a new clade supported by molecular phylogeny and comparative osteology (Siluriformes: Trichomycteridae). ZOOL ANZ 2021. [DOI: 10.1016/j.jcz.2021.05.008] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Comparative Osteology, Phylogeny and Classification of the Eastern South American Catfish Genus Trichomycterus (Siluriformes: Trichomycteridae). TAXONOMY 2021. [DOI: 10.3390/taxonomy1020013] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Trichomycterus has been considered for a long time to be the most problematic genus of the diverse neotropical subfamily Trichomycterinae. Recently, Trichomycterus was restricted to a clade from eastern South America supported by molecular data, but no unique morphological character state was found to distinguish it, making it difficult to allocate new species based on morphology alone. The objectives of this study were to conduct an osteological comparative analysis comprising a large sample of valid species of Trichomycterus, to conduct a total evidence phylogenetic analysis, combining osteological characters and a multigene database, and to propose an intrageneric classification based on the results of the phylogenetic analysis. Fifty-two osteological characters were combined with a multigene molecular data set of 2974 bp for 44 species of Trichomycterus, and 21 outgroups generated a well-supported phylogenetic tree, making it possible to delimit and diagnose intrageneric lineages, of which six subgenera are recognized. The high morphological diversity of osteological structures herein first reported for Trichomycterus from eastern South America is possibly related to some ecological specializations. This study shows that osteological characters combined with molecular data may be useful to consistently delimit and distinguish between trichomycterines, shedding light on the still persistent problems in trichomycterine systematics.
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