Molecular identification of the fish fauna from the pantanal flood plain area in Brazil

Shimabukuro-Dias, Cristiane Kioko; Silva, Guilherme José da Costa; Ashikaga, Fernando Yuldi; Foresti, Fausto; Oliveira, Cláudio

doi:10.3109/24701394.2016.1149826

Cited by 11 publications

(7 citation statements)

References 20 publications

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“…In specific groups, such as the Neotropical fish, studies have used the barcoding threshold (approximately 2%) proposed by Ward (2009) to delimit a wide-range of species (Rosso et al, 2012;Bellafronte et al,. 2013;Pereira et al, 2013;Gomes et al, 2015;Shimabukuro-Dias et al, 2016;Díaz et al, 2016). Nonetheless, given the great diversity of 6 e160147 [6] species, particularly related to life histories and complexity of environment, a fixed threshold value can under-or overestimate the correct number of MOTUs (Brown et al, 2012).…”

Section: Discussionmentioning

confidence: 99%

DNA barcoding confirms the occurrence of Rhamdia branneri and Rhamdia voulezi (Siluriformes: Heptapteridae) in the Iguaçu River Basin

et al. 2017

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DNA barcoding is a widely utilized molecular-based identification of species and taxonomic resolutions. Until recently, Rhamdia voulezi and Rhamdia branneri were considered species synonyms of Rhamdia quelen; however, morphological and cytogenetic analyses have suggested the validity of distinct species. Due to the absence of molecular taxonomy of R. voulezi and R. branneri, the objective of this study was to test its validity through traditional DNA barcoding and the GMYC (General Mixed Yule Coalescent) COI-based analyses in 19 specimens from the Iguaçu River Basin. In both methodologies, three MOTUs (Molecular Operational Taxonomic Units) were identified based on the estimated optimum threshold (OT = 0.77). The average inter-MOTU distance (NJ, K2P) between R. branneri and R. voulezi was 1.4%, and 0% intra-MOTU distance in both species. The two species identified as R. branneri and R. voulezi showed correspondence with taxonomic and morphological identifications. With regard to R. quelen, the average intra-MOTU distance was greater than OT (2.7%), indicating that this species can be formed by different MOTUs. We suggest that molecular and taxonomic studies should be employed concurrently in R. quelen, to prevent contamination of wild species by hybridizations. O DNA barcoding é uma ferramenta molecular precisa para a identificação de espécies e resoluções taxonômicas. Até recentemente, Rhamdia voulezi e Rhamdia branneri eram consideradas sinônimas de Rhamdia quelen, contudo caracteres morfológicos e citogenéticos têm apontado à validade de ambas. Devido à escassez de informações sobre a taxonomia molecular de R. voulezi e R. branneri, o objetivo do presente estudo foi testar a validade das mesmas através do método de DNA barcoding tradicional e GMYC (General Mixed Yule Coalescent), por meio da análise do gene COI em 19 espécimes do rio Iguaçu. Em ambos os métodos, três MOTUs (Unidades Taxonômicas Operacionais Moleculares) foram identificadas com base no ótimo threshold (OT = 0,77). A média inter-MOTU (NJ, K2P) entre R. branneri e R. voulezi foi 1,4%, com valores de 0% intra-MOTUs em ambas espécies. As duas espécies identificadas como R. voulezi e R. branneri apresentaram correspondência com a identificação taxonômica e morfológica dos respectivos vouchers. No que se refere a R. quelen, os resultados intra-MOTU foram superiores ao OT (2,7%), evidenciando a possibilidade de existirem diferentes MOTUs denominadas como R. quelen. Sugerimos que estudos moleculares e taxonômicos sejam empregados em R. quelen, para evitar a contaminação de espécies selvagens por hibridizações.Palavras-chave: Aquicultura, COI, Complexo de espécies, Jundiá, MOTU.

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Section: Discussionmentioning

confidence: 99%

DNA barcoding confirms the occurrence of Rhamdia branneri and Rhamdia voulezi (Siluriformes: Heptapteridae) in the Iguaçu River Basin

et al. 2017

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“…Cryptic species are defined as distinct evolutionary lineages not detectable with traditional taxonomic approaches, due to the absence of morphological differences ( Avise, 2000 ; Mallet, 2010 ). In the last decade, barcoding methods based on COI sequences have made possible their identification in several marine and freshwater fish species ( Ward et al, 2008 ; Lara et al, 2010 ; Puckridge et al, 2013 ; Mateussi et al, 2017 ; Okamoto et al, 2017 ; Ramirez et al, 2017 ; Shimabukuro-Dias et al, 2017 ). In Mugilidae evidences of cryptic species were inferred from mitochondrial tree topology, independent data from nuclear markers, and on the base of the geographic distribution of sister lineages ( Durand and Borsa, 2015 ).…”

Section: Discussionmentioning

confidence: 99%

Identification of a New Mullet Species Complex Based on an Integrative Molecular and Cytogenetic Investigation of Mugil hospes (Mugilidae: Mugiliformes)

et al. 2018

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Mullets are very common fishes included in the family Mugilidae, (Mugiliformes), which are characterized by both a remarkably uniform external morphology and internal anatomy. Recently, within this family, different species complexes were molecularly identified within Mugil, a genus which is characterized by lineages that sometimes show very different karyotypes. Here we report the results of cytogenetic and molecular analyses conducted on Mugil hospes, commonly known as the hospe mullet, from Ecuador. The study aims to verify whether the original described species from the Pacific Ocean corresponds to that identified in the Atlantic Ocean, and to identify species-specific chromosome markers that can add new comparative data about Mugilidae karyotype evolution. The karyotype of M. hospes from Ecuador is composed of 48 acrocentric chromosomes and shows two active nucleolar organizer regions (NORs). In situ hybridization, using different types of repetitive sequences (rDNAs, U1 snDNA, telomeric repeats) as probes, identified species-specific chromosome markers that have been compared with those of other species of the genus Mugil. Cytochrome c oxidase subunit I (COI) sequence analysis shows only 92–93% similarity with sequences previously deposited under this species name in GenBank, all of which were from the Atlantic Ocean. Phylogenetic reconstructions indicate the presence of three well-supported hospe mullet lineages whose molecular divergence is compatible with the presence of distinct species. Indeed, the first lineage includes samples from Ecuador, whereas the other two lineages include the Atlantic samples and correspond to M. brevirostris from Brazil and Mugil sp. R from Belize/Venezuela. Results here provided reiterate the pivotal importance of an integrative molecular and cytogenetic approach in the reconstruction of the relationships within Mugilidae.

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“…This same software was used to calculate the genetic distance within and between populations using the Kimura-2-Parameters (K2P) model [ 59 ]. Traditionally, a threshold of 2% genetic distance has been used to delimit species using COI [ 49 ], [ 38 ], [ 41 ], [ 60 ], [ 61 ]. Herein we assume this threshold and also estimated the phylogenetic relationships of samples to test the monophyly of nominal species.…”

Section: Methodsmentioning

confidence: 99%

Reappraisal of the systematics of Microglanis cottoides (Siluriformes, Pseudopimelodidae), a catfish from southern Brazil

et al. 2018

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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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Molecular identification of the fish fauna from the pantanal flood plain area in Brazil

Cited by 11 publications

References 20 publications

DNA barcoding confirms the occurrence of Rhamdia branneri and Rhamdia voulezi (Siluriformes: Heptapteridae) in the Iguaçu River Basin

DNA barcoding confirms the occurrence of Rhamdia branneri and Rhamdia voulezi (Siluriformes: Heptapteridae) in the Iguaçu River Basin

Identification of a New Mullet Species Complex Based on an Integrative Molecular and Cytogenetic Investigation of Mugil hospes (Mugilidae: Mugiliformes)

Reappraisal of the systematics of Microglanis cottoides (Siluriformes, Pseudopimelodidae), a catfish from southern Brazil

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