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.2015 Nov 30:5:17437.
doi: 10.1038/srep17437.

The fish diversity in the upper reaches of the Salween River, Nujiang River, revealed by DNA barcoding

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The fish diversity in the upper reaches of the Salween River, Nujiang River, revealed by DNA barcoding

Weitao Chen et al. Sci Rep..

Abstract

Nujiang River (NR), an essential component of the biodiversity hotspot of the Mountains of Southwest China, possesses a characteristic fish fauna and contains endemic species. Although previous studies on fish diversity in the NR have primarily consisted of listings of the fish species observed during field collections, in our study, we DNA-barcoded 1139 specimens belonging to 46 morphologically distinct fish species distributed throughout the NR basin by employing multiple analytical approaches. According to our analyses, DNA barcoding is an efficient method for the identification of fish by the presence of barcode gaps. However, three invasive species are characterized by deep conspecific divergences, generating multiple lineages and Operational Taxonomic Units (OTUs), implying the possibility of cryptic species. At the other end of the spectrum, ten species (from three genera) that are characterized by an overlap between their intra- and interspecific genetic distances form a single genetic cluster and share haplotypes. The neighbor-joining phenogram, Barcode Index Numbers (BINs) and Automatic Barcode Gap Discovery (ABGD) identified 43 putative species, while the General Mixed Yule-coalescence (GMYC) identified five more OTUs. Thus, our study established a reliable DNA barcode reference library for the fish in the NR and sheds new light on the local fish diversity.

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Figures

Figure 1
Figure 1. Map of locations sampled in this study.
The numbers of the locations refer to 1) Bingzhongluo, 2) Puladi, 3) Maji, 4)County Areas of Fugong, 5) Pihe, 6) Chenggan, 7) Liuku, 8) Hongqi Dam, 9)Mangkuan, 10) Xiaopingtian, 11) Sanjiangkou, 12) Longzhen Bridge, 13)Kongguang Village, 14) Manglong River, 15) Mangkuan River, 16) MangliuRiver, and 17) Longwang Pond. Locations 1–12 are sampling sitesin the main stem, and 13–17 are located in a tributary. Locationdetails and a list of the number of samples collected per site are providedin Supplementary Table S1. Mapwas created in the ArcGIS version 10.1 and modified in Microsoft Office.
Figure 2
Figure 2. Maximum intraspecific divergence compared with the nearest-neighbor distance for fish in the Nujiang River.
Only species with multiple sequences (Table S1) are presented. All of these species fall above the 1:1line, indicating the presence of a ‘barcodegap.’
Figure 3
Figure 3. NJ tree of 1139 COI barcodes based on the K2P model.
The framed clusters and the highlighted clusters in grey indicate specieswith a high cryptic diversity and species characterized by haplotype sharingor low interspecific distances, respectively.
Figure 4
Figure 4. Bayesian inference gene tree with delineated OTUs.
Grey rectangles represent species that share a COI lineage.
Figure 5
Figure 5. Haplotype networks of species with low interspecific divergences.
(a) Genus Creteuchiloglanis; (b) genus Schistura; and(c) genusSchizothorax. The bold numbers on the internodesindicate mutation steps, and the other numbers are the frequencies of eachhaplotype. A red empty circle indicates missing intermediate steps betweenobserved haplotypes.
Figure 6
Figure 6. NJ trees and mean conspecific distances of the three species with deep intraspecific divergences based on the K2P model for our COI sequences and the downloaded sequences.
(a)Abbottina rivularis; (b)Rhodeus ocellatus;and (c)Paramisgurnus dabryanus.
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References

    1. Chen Y. Y. The Fishes of the Hengduan Mountains Region, (Science Press, 1998).
    1. Chu X. L. & Chen Y. R. The Fishes of Yunnan, China. Cyprinidae. (Sciences Press, 1989).
    1. Fu J. et al. The ecological influences and protection measures in the Nujiang river hydropower development. Journal of Sichuan Forestry Science and Technology 33, 101–103 (2012).
    1. Jiang W. S., Ng H. H., Yang J. X. & Chen X. Y. A taxonomic review of the catfish identified as Glyptothorax zanaensis(Teleostei: Siluriformes: Sisoridae), with the descriptions of two new species. Zoological Journal of the Linnean Society 165, 363–389 (2012).
    1. Ng H. H., Jiang W. S. & Chen X. Y. Glyptothorax lanceatus, a new species of sisorid catfish (Teleostei: Siluriformes) from southwestern China. Zootaxa 3250, 54–62 (2012).

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