DNA barcoding for the identification of common economic aquatic products in Central China and its application for the supervision of the market trade

Shen, Yanjun; Kang, Jingliang; Chen, Weitao; He, Shunping

doi:10.1016/j.foodcont.2015.08.038

Cited by 27 publications

(10 citation statements)

References 46 publications

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“…Since the launch of an international campaign to DNA barcode the c.a. 33,900 fish species (FISHBOL, (Ward, Hanner, & Hebert, 2009)), the effectiveness of DNA barcoding to identify fish species is increasingly acknowledged (April, Mayden, Hanner & Bernatchez L, 2011;Dahruddin, Hutama, & Busson, 2017;Durand et al, 2017;Geiger et al, 2014;Hubert et al, 2008aHubert et al, , 2012Kadarusman & Hadiaty, 2012;Knebelsberger et al, 2015;Pereira, Hanner, Foresti, & Oliveira, 2013;Randall & Victor, 2015;Shen, Guan, et al, 2016b;Shen, Kang, et al (April, Mayden, Hanner, et al, 2011). In the present study, 195 species of the 238 species analysed (82%) were delimited using DNA-based methods and displayed a barcode gap on an individual basis.…”

Section: Discussionmentioning

confidence: 82%

“…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, ).…”

Section: Discussionmentioning

confidence: 99%

“…Landscape features such as fragmentation, however, proved to be a challenge to accurately delimit species through DNA barcodes (Geiger, Herder, & Monaghan, 2014;Keskin, Agdamar, & Tarkan, 2013;Knebelsberger, Dunz, Neumann, & Geiger, 2015). In the context of the YR ichthyofauna, a preliminary assessment of the effectiveness of DNA barcoding in identifying YR freshwater fishes confirmed its potential for conservation purposes (Shen, Guan, Wang, & Gan, 2016b;Shen, Kang, Chen, & He, 2016a). One of the key factors for the successful application of DNA barcoding is the availability of reliable DNA barcode reference libraries in the Barcode of Life Database (BOLD), (Ratnasingham & Hebert, 2007).…”

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confidence: 97%

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

Shen

Hubert

Huang

et al. 2019

Molecular Ecology Resources

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Intensification of inland fisheries and aquatic landscape conversion led to a drastic decline of fish populations in the Yangtze River (YR) during the last decades. This situation urges for the development of a large‐scale molecular assessment of YR ichthyofauna to further develop standardized methods of molecular identification for conservation and fisheries management purposes. We present here the results of a large‐scale campaign to DNA barcode YR freshwater fishes that succeeded in producing 1,424 new DNA barcodes for 123 species. Together with 1,406 sequences mined from BOLD and GenBank, a reference library including 2,830 DNA barcodes for 238 species was compiled. By using four DNA‐based species delimitation methods, RESL, ABGD, mPTP and mGMYC, 230 operational taxonomic units (OTUs) were identified and 195 species displayed OTUs that tightly match species boundaries. No barcoding gap was observed; however, and conflicting cases of species and OTU delimitation were identified. A total of 23 species with maximum intraspecific distances above 2% were detected and null genetic distances to the nearest phylogenetic relatives were detected in 11 species. Among those 23 species, 16 were represented by multiple OTUs amounting to 40 OTUs delineated. Several cases of multiple OTUs confined to species boundaries were detected suggesting the presence of overlooked species. A total of 18 OTUs, however, were shared by several species and particularly so for the Qinghai‐Tibet plateau endemic species. These results are discussed with reference to previous large‐scale DNA barcoding campaign and compared to previous phylogeographic studies in the YR.

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Section: Discussionmentioning

confidence: 82%

Section: Discussionmentioning

confidence: 99%

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confidence: 97%

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

Shen

Hubert

Huang

et al. 2019

Molecular Ecology Resources

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“…The natural range of the rapa whelk is the water areas of the Yellow, Bohai, East China Seas, and the Sea of Japan. Molecular surveys revealed high genetic diversity among the natural populations and the fact that this is not associated with geographic distance between populations (Chandler et al, 2008;Kim et al, 2012;Shen et al, 2016). Populations of the Far Eastern Seas have been affected by overexploitation and have rapidly decreased (Yang et al, 2008).…”

Section: Introductionmentioning

confidence: 99%

Adaptive strategy of Rapana venosa (Gastropoda, Muricidae) in the invasive population of the Black Sea

Slynko

Rabushko

2020

Biosys. divers.

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We conducted molecular-genetic and morphological studies on the veined rapa whelk Rapana venosa (Valenciennes, 1846) in the Crimean waters of the Black Sea in order to determine possible reasons of the invasive success of this mollusk. Molecular-genetic tests were performed using COI gene; the surveyed samples reliably identified to R. venosa species. We compared the data on initial (from the Far-Eastern seas) and some invasive populations. In the natural conditions of the Yellow, East China Seas, and the Sea of Japan, the genetic diversity of rapa whelk is high (Hd = 0.933, π = 0.002). In all the invasive populations of rapa whelk (Black Sea, European and North American), an extremely low level of haplotypic and nucleotide diversity was determined (Hd = 0.0, π = 0.0). Despite low values of genetic diversity, the invasive populations of rapa whelk are characterized by ecological success. We noted stable growth of populations, tolerance to diseases and parasites, effective reproduction, high fertility. This contradicts the main provisions of the population genetics theory of formation of edge of range populations, because usually only a small number of specimens of rapa whelk were introduced. The explanations of the unique condition of the invasive populations of rapa whelk, both from an ecological perspective (high resistance to fluctuations of hydrological factors and chemical pollution, absence of enemies, high fertility) and genetic perspective (high selective value of separate haplotypes settled in the new water areas) have not been confirmed. We determined that a very important factor for the naturalization of the rapa whelk at low genetic diversity is the intra-species morpho-ecological divergence. In the Crimean water area of the Black Sea, R. venosa was found to have two morpho-ecological forms associated with the peculiarities of the development of the proportions of the shell. Study of successful invasive species would allow timely and adequate reaction to new cases of introduction.

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“…Sequences for the same species are generally considered to be correctly identified when they form a monophyletic cluster on a neighbor-joining (NJ) tree with intraspecific distances that are below a given threshold (Srivathsan and Meier 2012). At present, this approach has proven to be highly efficient and reliable in many fish groups (Ward et al 2005;Hubert et al 2008Hubert et al , 2010Rock et al 2008;Keskin et al 2013;Loh et al 2014) and is regularly used for a variety of applications, such as fishery management, biodiversity assessments and conservation (Triantafyllidis et al 2011;Weigt et al 2012;Keskin et al 2013;Loh et al 2014;Shen et al 2016).…”

Section: Introductionmentioning

confidence: 99%

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

Shen

Guan

Wang

et al. 2016

Ecology and Evolution

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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.

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DNA barcoding for the identification of common economic aquatic products in Central China and its application for the supervision of the market trade

Cited by 27 publications

References 46 publications

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

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

Adaptive strategy of Rapana venosa (Gastropoda, Muricidae) in the invasive population of the Black Sea

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

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