Use of DNA barcode in the identification of fish species from Ribeira de Iguape Basin and coastal rivers from São Paulo State (Brazil)

Abstract

Species identification is a difficult task, ranging from the definition of the species concept itself to the definition of the threshold for speciation. DNA Barcode technology uses a fragment of the Cytochrome Oxidase I (COI) gene as a molecular tool that many studies have already validated as a tool for species identification. DNA barcode sequences for COI were generated and analyzed from 805 specimens. The General Mixed Yule Coalescent (GMYC) analysis recognized 99 independent evolution units, and the Barcode Index Numbers (BIN) approach pointed to the existence of 104 BINs (interpreted as distinct species). By cross-tabulating the results of all approaches, we identified 109 Molecular Operational Taxonomic Units (MOTU) by at least one methodology. In most cases (89 MOTUs), the genetic approaches are in agreement with morphological identification, and the discrepant results of MOTUs are in the complex groups, which have many morphological similarities but may represent species complexes.

DNA barcoding for identification of fish species from freshwater in Enugu and Anambra States of Nigeria

“…Therefore, we accept the hypothesis of selective neutrality. Average nucleotide frequencies detected were similar to those that were previously reported in other studies of 577 fish specimens with base nucleotide compositions of C (27.25%), T (30.74%), A (24.04%), G (17.97%) and A + T = 54.8 (Mabragan et al 2011); 79 species of fish with C (27.53%), T (29.40%), A (24.82%), G (18.04%) and A + T = 54.22% (Díaz et al 2016); two species of Hypophthalmichthys molitrix (A = 31•8%, C = 26•9%, G = 15•7%, T = 25•6%, A + T = 57•4%), and H. nobilis (A = 31•6%, C = 27•1%, G = 16•0%, T = 25•3%, A + T = 56•9%) (Li et al 2009); 89 fish species (A = 24.12%, C = 27•28%, G = 18•2%, T = 30•4%, A + T = 54.52%) (Henriques et al 2015); and the ones (A = 25.90%, C = 28.90%, G = 17.00% and T = 28.20%, A + T = 54.1) from Iyiola et al (2018). At the nucleotide level, the sequence alignment revealed much polymorphism at different consensus positions and this similar degree of variations had been previously observed in 28 species of fish (Persis et al 2009).…”

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

“…This method estimates the transition point on a tree in a molecular clock hypothesis, before which all nodes reflect species diversification events and after which all nodes represent a population coalescent process [ 45 ] and has become a widely used method for delimiting species based on single-locus data [ 47 , 48 , 62 – 66 ]. Although the GMYC method has a strong theoretical basis, it typically generates a high number of operational taxonomic units (OTUs) [ 67 , 68 ], and this result has already been reported for some Neotropical freshwater fish species (e.g., [ 48 , 64 , 69 ]. Although the genetic distance be an useful evidence to detect and delimit species, it should is not the unique source of information used for this purpose [ 70 – 73 ].…”

IsNematocharax(Actinopterygii, Characiformes) a monotypic fish genus?

“…The five clusters were consistently observed by NJ, BINs, GMYC, and bPTP analyses. Although these methods are based on distinct models, a growing number of studies confirm their reliability to infer putative species boundaries (Costa-Silva et al 2015;Henriques et al 2015;Lin et al 2015), with particular efficiency for the new algorithm implemented in the BIN System (RESL). Ratnasingham and Fig.…”