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

Abstract

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.

DNA barcoding reveals cryptic diversity in the underestimated genus Triplophysa (Cypriniformes: Cobitidae, Nemacheilinae) from the northeastern Qinghai-Tibet Plateau

“…Due to the extremely short time of species differentiation, ancestral traits are randomly fixed in the differentiated species [22,38]. Similar phenomena have been found in Psorophora [12], Syngnathidae [78] and Laemolyta [58], and mixed lineage cases are particularly common in plateau fish [65]. In this sense, to find evidence of reproductive isolation, nuclear genetic and ecological data must be combined for further research [6,45,70].…”

“…Although most of the values obtained in this paper are above 1.47% (14 of 18 MOTUs, Table 2), the maximum threshold value of related species detected between the obtained MOTUs is 0.40%, and some species have shared haplotypes. The existence of haplotype sharing among different species of plateau fishes may be related to complex species differentiation mechanisms or convergent evolution associated with local adaptation [13,65]. A lower threshold of genetic distance may be obtained when the genetic relationships between different species within a genus are analysed.…”

“…These values were used to calculate the maximum, minimum and mean intraspecific and interspecific MOTU distances [57]. The average K2P intraspecific distance was defined as the average within each nominal species, the maximum K2P intraspecific distance was defined as the largest distance observed between sequence pairs within a nominal species, and the barcoding gap was checked by the intraspecific and interspecific genetic distances [65].…”

Assessing species diversity of Coral Triangle artisanal fisheries: A DNA barcode reference library for the shore fishes retailed at Ambon harbor (Indonesia)

“…The usefulness of DNA barcoding to identify fish species is widely accepted with nearly 90% of the species analyzed having their boundaries aptly captured by DNA barcodes in previous studies (April, Mayden, Hanner, & Bernatchez, ; Hubert et al, ; Knebelsberger, Dunz, Neumann, & Geiger, ; Shen et al, ; Weigt et al, ). In the present study, only six cases of shared haplotypes between species were detected.…”

DNA Barcoding Reveals Cryptic Diversity in the Genus Triplophysa (Cypriniformes: Cobitidae, Nemacheilinae) from the Northeastern Qinghai-Tibet Plateau

“…Although most of the values obtained in this paper are above 1.47% (14 out of 18 MOTUs,Table 2), the maximum threshold value of related species detected between the obtained MOTUs is 0.40%, and some species have shared haplotypes. The phenomenon of sharing haplotype among the plateau shes may be related to the complicated mechanism of speciation and differentiation or the convergent evolution of local adaptation(Shen et al, 2019;Chen et al, 2020). A relatively low threshold of genetic distance may be obtained when the intraspecies relationships within a genus are analysed.…”