DNA barcoding of gobiid fishes (Perciformes, Gobioidei)

Abstract

Gobiids constitute a major proportion of fish population in both tropical and temperate freshwater as well as marine ecosystem. Due to their small size, cryptic ecology and ambiguous morphological characters, gobiids diversity was not documented completely. In this study, DNA barcodes were generated for 11 species of gobiids, collected from the Ashtamudi Lake, India. The mitochondrial COI gene was amplified using universal primers and the resulted 650 bp amplicon was sequenced. The COI barcodes clearly distinguished all the species with high interspecific genetic distance values than intra-specific values based on K2P (Kimura 2 Parameter) model. The average genetic distance (K2P model) within species, genus and family was 1.2%, 22.2% and 25.3%, respectively. In addition to barcode-based species identification system, Nucleotide Diagnostic (ND) characters specific for species were identified. The Neighbor-Joining tree revealed distinct clusters shared by the species of same genera.

Identification of gobies (Teleostei: Perciformes: Gobiidae) from the North and Baltic Seas combining morphological analysis and DNA barcoding

“…Thus far, Gobiidae DNA sequences have been used to analyse phylogenetic relationships among taxa (Thacker & Roje, ; Agorreta et al ., ; Tornabene, Chen & Pezold, ) or to investigate phylogeographical patterns at the population level (Gysels et al ., , b). Furthermore, DNA sequences were used for species identification based on divergence of a defined part of the mitochondrial cytochrome c oxidase subunit I (COI) gene (Hyung‐Bae, Seung‐Ho & Ho, ; Viswambharan et al ., ). This technique, known as DNA barcoding (Hebert et al ., ), has already proven its utility as a molecular tool for species identification throughout all major fish taxa, including species of marine as well as freshwater ecosystems from different geographical regions (Ward et al ., , ; Hubert et al ., ; Steinke et al ., ; April et al ., ; Mabragaña et al ., ; Cerutti‐Pereyra et al ., ; Costa et al ., ; Zhang & Hanner, ; Keskin & Atar, ; McCusker et al ., ; Geiger et al ., ; Knebelsberger et al ., ).…”

Spatial overlap of shark nursery areas and the salmon farming industry influences the trophic ecology of Squalus acanthias on the southern coast of Chile

“…One approach is DNA barcoding using universal primers to amplify part of target genes (Holmes, Steinke, & Ward, ; Ward et al., ). This approach is similar to the traditional morphology‐based methods, where species identification is based on the presence or absence of a distinct morphological feature (Viswambharan et al., ). In our study, the use of the cytochrome c oxidase subunit 1 gene ( Cox1 ) as a barcoding sequence allowed us for the first time to unambiguously identify S. acanthias as the dogfish species in the bycatch of artisanal fisheries in the region.…”

“…where species identification is based on the presence or absence of a distinct morphological feature (Viswambharan et al, 2015). In our study, the use of the cytochrome c oxidase subunit 1 gene (Cox1) as a barcoding sequence allowed us for the first time to unambiguously identify S. acanthias as the dogfish species in the bycatch of artisanal fisheries in the region.…”

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“…The differences between individuals of the same species often vary from species to species but usually low (~ 1%). For example, this value was 1.2% for India gobies (Viswambharan, et al, 2013), 0.3% for fish Vietnamese gobies (Thao, & Yen, 2015). Totally, it can be clearly that the genetic distance results proved that fish collected in Ha Giang and Phu Tho differed to fish collected from RIA1.…”