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

Chen W, Ma X, Shen Y, Mao Y, He S - Sci Rep (2015)

Bottom Line: 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.

View Article: PubMed Central - PubMed

Affiliation: The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei, 430072, China.

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.

No MeSH data available.


Related in: MedlinePlus

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.
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f3: 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.

Mentions: The NJ tree derived from the complete barcode dataset contained 43 species clusters(including the singleton species) supported by bootstrap values of ≧91%(Fig. 3). Four species (A. rivularis, C.macropterus, P. dabryanus, and R. ocellatus) formed twodistinct clusters supported by high bootstrap values (>98%), which indicatesa high degree of cryptic diversity and possibly the occurrence of cryptic species(Fig. 3, S1,framed clusters). Within this group, C. macropterus was characterized by twodistinct geographical splits, despite a low mean intraspecific divergence (0.52%K2P); one of these splits contained specimens from the main stem, and the othersplit contained specimens from the tributaries. Moreover, the NJ tree also revealedthree cases of haplotype sharing between species (Fig. 3, S1, groups highlighted in grey). The lackof divergence observed in Schistura and Schizothorax is particularlyintriguing because these genera involve three and five species, respectively,included in only one cluster per genus.


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

Chen W, Ma X, Shen Y, Mao Y, He S - Sci Rep (2015)

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.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4663501&req=5

f3: 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.
Mentions: The NJ tree derived from the complete barcode dataset contained 43 species clusters(including the singleton species) supported by bootstrap values of ≧91%(Fig. 3). Four species (A. rivularis, C.macropterus, P. dabryanus, and R. ocellatus) formed twodistinct clusters supported by high bootstrap values (>98%), which indicatesa high degree of cryptic diversity and possibly the occurrence of cryptic species(Fig. 3, S1,framed clusters). Within this group, C. macropterus was characterized by twodistinct geographical splits, despite a low mean intraspecific divergence (0.52%K2P); one of these splits contained specimens from the main stem, and the othersplit contained specimens from the tributaries. Moreover, the NJ tree also revealedthree cases of haplotype sharing between species (Fig. 3, S1, groups highlighted in grey). The lackof divergence observed in Schistura and Schizothorax is particularlyintriguing because these genera involve three and five species, respectively,included in only one cluster per genus.

Bottom Line: 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.

View Article: PubMed Central - PubMed

Affiliation: The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei, 430072, China.

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.

No MeSH data available.


Related in: MedlinePlus