DNA barcoding and evaluation of genetic diversity in Cyprinidae fish in the midstream of the Yangtze River

Abstract

The Yangtze River is the longest river in China and is divided into upstream and mid‐downstream regions by the Three Gorges (the natural barriers of the Yangtze River), resulting in a complex distribution of fish. Dramatic changes to habitat environments may ultimately threaten fish survival; thus, it is necessary to evaluate the genetic diversity and propose protective measures. Species identification is the most significant task in many fields of biological research and in conservation efforts. DNA barcoding, which constitutes the analysis of a short fragment of the mitochondrial cytochrome c oxidase subunit I (COI) sequence, has been widely used for species identification. In this study, we collected 561 COI barcode sequences from 35 fish from the midstream of the Yangtze River. The intraspecific distances of all species were below 2% (with the exception of Acheilognathus macropterus and Hemibarbus maculatus). Nevertheless, all species could be unambiguously identified from the trees, barcoding gaps and taxonomic resolution ratio values. Furthermore, the COI barcode diversity was found to be low (≤0.5%), with the exception of H. maculatus (0.87%), A. macropterus (2.02%) and Saurogobio dabryi (0.82%). No or few shared haplotypes were detected between the upstream and downstream populations for ten species with overall nucleotide diversities greater than 0.00%, which indicated the likelihood of significant population genetic structuring. Our analyses indicated that DNA barcoding is an effective tool for the identification of cyprinidae fish in the midstream of the Yangtze River. It is vital that some protective measures be taken immediately because of the low COI barcode diversity.

DNAbarcoding of economically important freshwater fish species from north‐central Nigeria uncovers cryptic diversity

“…The success rates of DNA barcoding approach in our study (95.60%) was higher than the 93% success rate reported for Canadian freshwater fish (Hubert et al., ) and the 90% success rate reported for North American freshwater fish (April, Mayden, Hanner, & Bernatchez, ). However, our DNA barcoding success rate was lower when compared to 100% success rate reported by Shen, Guan, Wang, and Gan () and 98.30% success rate reported for Indian freshwater fishes (Lakra et al., ). In most cases, our study shows that COI sequences effectively clustered most of the conspecific and congeneric species.…”

DNA barcoding the ichthyofauna of the Yangtze River: Insights from the molecular inventory of a mega‐diverse temperate fauna

“…Since the launch of an international campaign to DNA barcode the c.a. 33,900 fish species (FISHBOL, (Ward, Hanner, & Hebert, )), the effectiveness of DNA barcoding to identify fish species is increasingly acknowledged (April, Mayden, Hanner & Bernatchez L, ; Dahruddin, Hutama, & Busson, ; Durand et al, ; Geiger et al, ; Hubert et al, ; Kadarusman & Hadiaty, ; Knebelsberger et al, ; Pereira, Hanner, Foresti, & Oliveira, ; Randall & Victor, ; Shen, Guan, et al, ; Shen, Kang, et al, ; Victor, Valdez‐Moreno, & Vásquez‐Yeomans, ; Ward, Zemlak, Innes, Last, & Hebert, ; Weigt, Baldwin, & Driskell, ; Winterbottom et al, ). Maximum intraspecific genetic distances are usually lower than the distances to the nearest phylogenetic relative, and large‐scale assessment previously reported that this barcode gap is observed for nearly 90 per cent of the species examined for well‐known ichthyofauna (April, Mayden, Hanner, et al, ).…”

DNA barcoding fishes from the Congo and the Lower Guinean provinces: Assembling a reference library for poorly inventoried fauna

“…Other overlooked taxa may be distinguished by DNA barcode divergences of 0.7%–3.8% within nine morphospecies present in a single province. The contribution of DNA barcoding for the detection of new taxa was acknowledged in most DNA barcoding campaigns focusing on large river basins (Decru et al, ; Hubert et al, ; Nascimento et al, ; Pereira, Pazian, Hanner, Foresti, & Oliveira, ; Shen, Guan, Wang, & Gan, ). Multiple lineages were suspected within Enteromius miolepis on the basis of DNA barcodes.…”